I just saw this movie, and found it ok but severely shallow in many ways. For one, Maher not only buys into the "Muslim = terrorist" concept as stated already, he also confronts normal, everyday people who are Muslims (some even Americans), interpreting their "it's a peaceful religion" defense as deliberate LYING. Lying to themselves, maybe, but to portray it as some kind of conspiracy involving every Muslim on Earth? That's quite a stretch.
I also noticed that Maher doesn't ask any of the hard questions when it comes to Israel. In fact, quite the opposite - he interviewed a rabbi who's in "Jews Against Zionism," and completely attacked the guy. He also tried to interrupt the rabbi constantly, but the rabbi wouldn't have it ("Let me finish, let me finish," he said throughout). Maher then walked out on the interview in disgust; it's the only time in the film that an interview provoked such a reaction from him.
Interestingly, in the DVD extras Maher interviewed David Icke, who was allowed to give a far more comprehensive defense of his Reptilian theory than the rabbi was of his anti-Israel ideas. Granted, the Icke interview didn't make it into the actual movie... but it's still interesting that Maher gave Icke a more-or-less fair hearing, yet had a strong negative reaction to an anti-zionist Jew.
Something just smells funny about this movie. If Maher is sincere, he's at least filling the "useful idiot" role very well.