In particular, the argument on scientific information in a religious text that is unambiguous and beyond the knowledge of the writers at the time is particularly strong. If Jesus had rambled on about quantum mechanics instead of fishes and loaves, I'd still be Catholic (probably a nun to boot).
There is also a companion article that discusses how to argue with an atheist (written from an annoyed atheist perspective). Of particular note is the following passage:
The problem is not that atheists are inherently more difficult to communicate with productively, but that there are many religious organizations that persist in actively spreading misinformation about atheism. These groups are not interested in an open debate or an impartial comparison of the facts; their goal is to retain members by casting the alternatives in a poor light. They have no incentive to give the opposing viewpoint a fair hearing, just as a commercial touting the benefits of a product is not going to objectively list the strengths of its competitors. While these tactics may help keep members in line by convincing them that the alternatives are unpalatable, they often fail utterly when used against real atheists; many believers have found to their surprise and chagrin that we are not the arrogant, amoral misanthropes their preachers have told them we are.
I think this goes far to explain why atheists are mistrusted and demonized.