I’m way late to this, but just saw it last night and wanted to weigh in briefly. I had planned to address several of the key problems, as well as acknowledge its (few) pleasures as a movie, but Steve Waldman did the yeoman’s job already. Read each of his pointed critiques (the full list is here).

The main problem with “Religulous” is that it seems to think, or at least it acts like it thinks, that it’s really taking on the whole subject of religion. But my five-year-old’s pinky finger could contain all that Bill Maher and director Larry Charles understand about religious belief. Maher has no sense of what motivates religious persuasions; his line of questioning in the film is often wandering and confused, such as when he tries to dog Francis Collins on the issue of the historicity of the gospels. Maher doesn’t grasp that his main quibble is with fundamentalism–he thinks that if you’ve got faith, any faith at all, and you follow that faith to its logical conclusion, sooner or later you’ll want to kill someone. 
Maher also doesn’t understand that what he really hates is the mirror. The fundies he decries are a lot like him–opinionated, unmovable, unable to listen to other points of view, uninterested in anyone’s paradigm but their own. He doesn’t seek to understand, as he purports to do. He seeks to preach and destroy. “Religulous” ends with a long sermon by Maher decrying the evils of faith and touting the liberation possible in disbelief, and it’s the most honest moment in the whole movie. Maher is seeking converts to fundamentalist Maherism, and everyone who won’t convert will be damned.  
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