I don't believe in a god and I don't have any problem with Christians or the religious. I can't speak for Atheists, only myself.
What I have a problem when someone else's belief system impinges on my rights. For instance, the fact the GW thinks that God is guiding him has led us into a terrible mess in Iraq and elsewhere. I'm also not thrilled when religious beliefs try to dictate scientific principals based on a holy book... or some absolutes or how "I" should live my life. Believe it or not, most atheists are quite nice and moral people, but I think they express themselves angrily on the web...
And yes, I'll admit that after being a Christian for the first 14 years of my life, I realized that the Bible might not be the literal word of a god. So since then, belief has seemed to me like something that people do because they've been conditioned or conned into it... I fully admit I may be wrong, and I've been there, so I harbor no ill will. Most of my friends are believers. I know this doesn't really answer your question, but you should know that not all non-theists are hostile, and you even say that in your question.
Bottom line - some people may feel like they need to defend their view point... they could be bitter about what it was like to be religious... Might be that they don't like it when someone isnt' being logical, that it hurts their brain. And sometimes it's because people see danger in blind belief, an actual fear of the results of blind faith... 9/11... or the milder versions that happen every day... children dying because parents believe in Faith healing, for instance.