Bill Maher declares at the outset that he's just a reasonable man who seeks to raise the status of "doubt." While religion sells a silly/dangerous "invisible product," he says, "my product is doubt."
But by the end he declares, with fervor that would make Jimmy Swaggart proud, "Religion must die if mankind is to live." There is no doubt, no shades of gray. There are no examples of religion ever doing anything good, ever. He casts his opponents as not merely mistaken but grotesque and dangerous to your very existence.
Maher's product is not doubt. It's certainty -- a black-and-white world view that demonizes religion in the same way that some religious fundamentalists demonize those who differ from them.
Maher is a secular fundamentalist.
Now, I also happen to think t he movie was often funny and scored some direct hits on religious snake oil salesmen. But on balance, he undercut his case by ignoring history that didn't fit his narrative, taking quotes out of context, and generally engaging in some of the same deceptive practices he excoriates among religious zealots.