This the explicit premise of the movie, an atheist call to action. A further premise I would add is the following: We're not letting the Evangelicals be the only ones who don't listen to, and badger, people who disagree with them - now we can be condescending know-it-alls too!
It reminded me of the famous British atheist and Oxford professor, Richard Dawkins. Specifically a film I saw at the Roxie a few years ago that was a compilation from his BBC television series...I believe it was called, "Root of All Evil?" in which Dawkins proceeded to cross the globe harrassing religious people and in so many words, telling them they're stupid. Actually even though Dawkins is obviously an influence (e.g., looking for 'evidence' of miracles, citing the story of Lot's daughters from the Bible), he's almost subtle compared to Maher.
Maher let very few of the people he spoke to get a word in edge-wise. He spoke very quickly, asking for evidence, for example, for the virgin birth. When the person opened their mouth to reply, he would rapid-fire several more questions. Maher got up and walked out on the one guy who wouldn't let himself be interrupted. To me it looked like his primary purpose was to make everyone look like an idiot, thereby "proving" that atheists are superior, and religion is bad.
Religion helps a lot of people. I'm not saying it's perfect or unproblematic - in fact religions cause and continue to cause a great deal of harm in the world. But it's obvious that both Maher and Dawkins do not really understand what they are criticizing and this is probably the fundamental flaw. To me, Maher looked like an ass in most of the film, exemplifying some of the intolerance he is perhaps meaning to criticize.
But maybe this kind of thing is good, and necessary: Fundamentalist Christianity has a lot of power in this country, and us 16% types should no doubt start expressing ourselves more without being afraid. I hope that Dawkins and Maher are right and that their films do some good. May atheists claim their birthright, and acquire even a fraction of the zeal possessed by their monotheistic counterparts.
References
Religulous on IMDB
Richard Dawkins on Wikipedia
Story of Lot on Wikipedia