Actually, you seem to have been misinformed. In general, atheists are annoyed by 6 things... not 3:
* gullibility
* irrationality
* willful ignorance
* self-delusion
* intellectual dishonesty
* drooling stupidity
Now... those things are annoying, even when encountered one-at-a-time... but since religion encapsulates ALL SIX of those into one convenient package... well that makes religious belief REALLY annoying. Let's just take a look at Genesis, so you can see what I mean...
You don't need to be possessed of the 'Secret Magical Decoder Ring'... ehhh... oops... sorry... scratch that... I mean you don't have to be possessed of the 'Holy Spirit' in order to understand Genesis. It takes no more that an attentive (and rational) reading of the first few verses of Genesis (with your 'rational' goggles on) to realize that it... and all that depends from it... is myth. In a rational reading of Genesis, a literal interpretation is required in order for it to make sense of it... no metaphors... no allegory... no hidden meanings. Otherwise, it makes no sense at all.
In biblical times, people thought that the earth and heaven were all that there was... and that the earth was essentially a 'terrarium'. They thought that the sky was a solid object, called the 'firmament', and that the sun, moon, and stars were affixed to it. So, essentially, heaven is 'on the other side of the sky'.
The story of Genesis is comprised of the myths, fairy tales and fantastical delusions of a superstitious and ignorant (lacking in knowledge) bunch of Bronze Age fishermen and wandering goat herders, sprinkled with folk-tales lifted from the oral traditions of their own and other cultures, and crafted into a pseudo-history. This the foundation and basis for the Abrahamic cults of desert monotheism... Judaism, Christianity and Islam.
The cosmological aspects of Genesis are perfectly understandable, if you contemplate them in the proper context... that context being profound ignorance (lack of knowledge) and superstition... and take 'Zeitgeist' (the spirit of the times) into account.
At the time the bible stories were concocted, the perception was that the earth and the sky (which included an imagined heaven) were all that there was. Why? Because they had no reason to think otherwise. Today, as we advance science, we stand upon the shoulders of all the scientists that came before. Back then there were no shoulders to stand upon... so they did the best they could with what they had... their senses, their imaginations and their appreciation of a good story. They were desperately trying to answer profound questions relating to their world and their existence... questions like "What holds the sky up?", and "Where did we come from?" There was no choice beyond 'making up' the answers.
* They had no concept of 'outer space', and so they conceived that in the beginning all that existed were dark waters.
* They had no concept of 'nothingness'. Remember, the concept of 'zero' wasn't invented (discovered?) until thousands of years later. With that in mind, the term 'void', as it is employed in Genesis, can not refer to 'nothingness'... it can only be applied in its alternative definition, which is 'empty'. So, the waters were dark, formless and void (empty - devoid of content).
* They thought that all of creation consisted of the earth and an unseen 'heaven', and they thought that the sky was a 'thing'... a substantive 'firmament' that was created by god to separate the waters and differentiate earth from heaven, when both were created. (By the way... this 'dividing the waters' bit gave them a credible way to explain why the sky is blue.)
# They had no idea that Earth was a planet, orbiting a star.
# They had no idea that there is no firmament... that the sky is not a 'thing'.
(If you don't believe that they thought the sky was an object... a solid barrier... consider the Tower of Babel, which they were (supposedly) building to reach heaven. Apparently, God ALSO thought that the sky was an object, since the tower vexed him so much that he confounded their speech, in order to disrupt their project and keep them from reaching his domain. God apparently know not know the actual configuration of the universe that he created.)
* They thought that the sun was a light that god had placed upon the 'firmament' to differentiate night from day.
# They had no idea that the sun is a star... the center of our solar system.
# They had no concept of 'stars' in the same sense that we understand them today... and certainly did not know that there are other stars like our sun.
* They had no idea that night and day were a consequence of the earth's rotation.
* They thought that the moon was a 'lesser' light that god had caused to travel across the firmament to enable man to differentiate the seasons, and provide illumination at night.
# They had no concept of the moon as a satellite.
* They thought that the stars were tiny lights that god had placed upon the firmament to provide for omens. (Some people of that time thought that the stars were 'holes' in the fabric of the firmament, which allowed the 'light of heaven' to shine through.)
# They had no idea that the stars were suns, just like our own sun.
# They thought the eyeball-visible planets (Mercury, Mars, Venus, Jupiter, Saturn) were 'wandering stars'.
# They had no idea that the planets were actually sun-orbiting bodies, just like earth.
* They had no idea that the earth, itself, is a planet.
# They had no clue as to the actual nature of the earth, our solar system, the place of our solar system in the galaxy... or even of the existence of our galaxy. (Up until very recently, we didn't even know that there even WERE other galaxies. Our galaxy, when it was first known that there actually WAS a galaxy, was thought to comprise the whole universe.) From their perspective, the 'earth' (covered by the 'firmament') and 'heaven' (i.e., whatever existed on the other side of the sky) represented all that there was. A terrarium.
I do not say these things to disparage what they thought back then. They were trying to do what science is trying to do today... trying to understand nature and reality. Today, we have technology and disciplined meta-procedures (scientific method) to help us extract answers from nature.
Back then, they did not.
Today, we have 'theories' to provide a consistent explanatory framework for what we are able to observe in nature, supplemented and validated by the additional information that we are able to extract from nature by means of our technology, our disciplined methods and our intellectual tools (mathematics, logic). Most of our theories are incomplete, so we continue to work on them... because we KNOW that they are incomplete.
Back then, they did not have disciplined methods, and they did not have the technology to extract answers from nature. The only information they had access to was what they could see with their own eyeballs. There was no technological knowledge base or scientific context in which to interpret their observations, so they had to appeal to their imaginations... and the 'supernatural'... in order to make sense out of what they saw. Actually, what they really achieved was deluding themselves into thinking that they knew the truth. Amazingly, over time, their delusions have become codified, institutionalized, and incorporated... complete with franchises.
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"The greatest obstacle to discovery is not ignorance... it is the illusion of knowledge." ~ Daniel Boorstin
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Basically, Genesis... and the very concept of god(s)... can be thought of as a 'hypothesis', concocted by people who were constrained by lack of technology, methodology and intellectual tools... although they don't seem to have been constrained by lack of imagination. Over time, though, the elements of this 'hypothesis' have been proven to be WRONG. The sky is NOT a solid object with a supernatural realm and a whole bunch of water on the other side of it. The lights in (actually, 'on') the sky are NOT there for signs, portents, omens, dividing day from night and differentiating the seasons. And all the while god was creating this terrarium, and fashioning Adam from a dust-bunny, the Mesopotamians were learning how to brew beer.
Today, we try to interpret Genesis in the context of what we KNOW about the universe... galaxies, stars, planets, moons, gravity, orbits, inclination of the earth's axis, planetary rotation, accretion disks, supernovae, solar nebulae, etc. They problem is that Genesis CAN'T be interpreted in terms of those things, because Genesis was written by ignorant men, based on oral traditions and their own imaginings, and those men DID NOT KNOW about ANY of those things. They could only write about what they could see and what they could imagine about the reasons that lay behind what they saw. In any event, it provided them with a mechanism to quell the innate anxiety that comes with fretting about how and why they came to be here... cognitive dissonance... and achieve cognitive harmony. Key point here... 'self-delusion' cures cognitive dissonance just as well as 'knowledge' does.
They imagined wrong.
So... the cosmological aspects of Genesis require a literal interpretation... no metaphors... no allegory... no hidden meaning. We don't need to be possessed of the 'Secret Magic Decoder Ring'... er... scratch that... I mean we don't have to be possessed of the 'Holy Spirit'. The key, though, is in understanding that the literal interpretation DOES NOT LEAD to a description of the way things ARE... it leads to a description of the way they THOUGHT things are, and how they got to be that way. It leads to a naive description of reality, concocted by people who were doing the best they could with what they had... and that INCLUDES the stories of Adam and Eve, Noah's flood, the Tower of Babel, and all the rest. Understanding that, it is easy to appreciate Genesis (and the bible in general) for what it actually is... a piece of primitive literature.
Let's recap: There is an all-powerful magical being who got bored and divided a previously-existing big glob of water... one side of his divider (the firmament... i.e., the sky), with half of the water, becomes heaven. From the water on the other side of the solid divider, he brings forth dirt. Then he abracadabras living things into existence, populating this clump of dirt and water. Then he speckles his divider with a few thousand little lights (like sprinkles on a Christmas cookie), to interpret for signs of things-to-come, a really big light so they could tell if it was day or night, and a smaller light so they could tell what season it was. While all of this was going on, a few hundres miles away... in the REAL universe... the Mesopotamians were making beer. Other stuff ensues, causing this magical dude to get honked off, so he releases all the water on HIS side of the sky, completely douching his sandbox world... except for a few creatures for whom he has a lingering fondness. (Let that be a lesson to them.) There's lots more... but it is comprised of nothing more than equally silly details. The whole thing reminds me of an 8-year old kid, at noon, hunched over an ant-hill with a magnifying glass... roasting ants.
Apologists have had a lot of fun with this, trying to explain how 'revealed knowledge', which was once 'divine TRUTH', have become allegories and metaphors, as these 'truths' have been bumped aside by REAL knowledge. This is how the 'God of the Gaps' was born.
As these myths and misconceptions have been dispelled, over the course of thousands of years, god has been reduced from an all-powerful being who could create a whole universe at a whim... i.e., brought forth some dirt from some water, and put a dome over it... to a 'God of the Gaps', who lurks in an ever-decreasing network of cracks and crevices that are still waiting to be filled in by knowledge. These cracks and crevices are defended by a stalwart army of 'believers', fighting a rear-guard action against knowledge and reason. Their tactics mainly consist of throwing up roadblocks on the path to knowledge, which they stand behind, waving their arms, and loudly proclaiming: "No... no... that ain't so... god did it." And every time a new piece of knowledge emerges, the God of the Gaps scurries away like a cockroach when the kitchen light gets turned on, searching for a new crevice to cower again... until the next time...
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"Myth has been needed precisely because we were not in a position to understand the universe on its own terms, through the language of natural law and direct examination of its workings on a material, rational level. Once that process of understanding is completed - and we are well on our way to achieving that - the use of myth can be discarded. Its continuing retention is already proving to be counter-productive." - Earl Doherty