First of all, we have to be careful to avoid what's called the genetic fallacy. The genetic fallacy says that a belief is false due to it's origins.
For example, imagine a man, Jones, who looks at a broken clock. The broken clock reads 12:30, but Jones doesn't know that the clock is broken and, in order to discover what time it is, Jones looks at the clock. Coincidentally, it is 12:30. So Jones now believes that it is 12:30, because he looked at a broken clock that, coincidentally, read 12:30.
Now, if Jones asserted "It is 12:30" would it be valid for me to respond "It can't be 12:30 because you were looking at a broken clock!"? No, that would be committing the genetic fallacy on my part. The fact that Jones acquired the belief without very good reasons, all things considered, doesn't mean his belief is false.
Likewise, if Christians believe in God because they are afraid of going to hell, that doesn't tell us anything about whether or not God exists or hell exists.
Furthermore, *if* there is a God who sends unbelievers to hell, then why should we think there is anything wrong with being afraid of going to hell?
Think of it this way: if you try to rob a bank and I say "Don't do that, or you'll be caught and thrown in prison," would you think my morality is fear based? Would you think that going to prison is an invalid motivator as to why you should not rob a bank?
If there is a system of law that sends you to prison for bank robbing, then it seems perfectly valid to use that as a motivator to refrain from bank robbing and it seems perfectly valid for me to point that out to would-be bank robbers.
The fact that punishment exists within our society as a deterrent to crime doesn't make our society fear based. Likewise, I don't see why divine punishment makes a religion fear based. And, furthermore, I don't see why refraining from an action or believing a proposition because you are afraid of the consequences is somehow negative or invalidates the action or proposition.
So when you say "do you honestly believe that there is one true God? Or are you just covering your bases..." this looks like a false dichotomy to me. Just because someone accepts Christ because they are afraid of God's punishment doesn't mean that they don't honestly believe "that there is one true God".
Finally, you ask: "And if you really do believe in God, how do you know that you have chosen the right religion?"
This question doesn't make much sense to me. I suppose you're trying to give the Christian some sort of epistemic angst like "Oh, no! there are so many religions... maybe I've chosen the wrong one... maybe I can't know which is the right one..." etc.
But this tactic, if it works at all (it doesn't), can work just as well against your own position: If you are an atheist, how do you know that you have chosen the right form of atheism? What if idealism is true? What if penrose-platonism is true? What if materialistic naturalism is true? Should I be an instrumentalist or a realist? Should I be an epiphenomalist? etc etc.
Of course, just as there isn't one form of religion, so there isn't one form of atheism (or one form of anything for that matter). Whatever significance this fact has for religion it equally has for atheism. If you can consider for a moment why you have chosen your worldview, then you should be able to answer for yourself why Christians have chosen their own worldview: basically, because it makes sense to them.