I've been thinking about this movie for a few days. As an atheist, this movie never sat right with me. The closing message was almost crazy to hear. The interviews didn't seem to make any point.
I found an opinion article that does a good job of arguing against the shallow premise of the movie. Though this author is a religious man, he does not fight fire with fire. He creates a stance that you can agree on without having to believe in anything.
Maher's mockery misses the point - Los Angeles Times