And therein lies the rub, I think. He doesn't. And I agree with all your other points.
I don't know, anytime I see Maher he just seems to have this ridiculous (and ridiculously unfounded) arrogance to him. He really seems to think he's an expert on just about everything, which he's clearly not. Just as one example off the top of my head, on his show one night they were talking about the airline industry - which, as an aviation operations major, I know a little about - and for some reason which I truly cannot understand, he was outraged by the idea that airlines outsource maintenance. He seemed to think it was some major scandal he was uncovering, and some of the other things he said in that show also demonstrated a similar total lack of knowledge on the subject matter.
Based on what I've seen about his movie (mostly just him talking about it on the Daily Show), it seems to be more of the same: Maher ridiculing people in conversations about subjects he clearly has little grasp of, in this case, the theology and philosophy of religion. I think you could make the argument that the film illustrates how poorly religious people understand their own religion, but you could make that argument equally well about any number of things other than religion, so it's not particularly insightful, really.
Another thing that frustrates me (going back to his show now), is the guest panel he always has - generally like 3 random celebrities or pseudo-celebrities who are in no way qualified to discuss whatever they're discussing and one person who is...just barely. I mean, I love Seinfeld as much as the next guy, but who really cares what Jason Alexander's opinion on reforming public education is?
Also, he's a bad comedian. Terrible delivery. And it doesn't help that he seems so amused by himself.