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First, it is pointless to get offended by Maher's simplistic depiction of religion. I try to remind myself, whenever he goes off on one of his anti-religion rants, that he's not talking about me. He thinks he's talking about me, but I know that the faith I practice is nothing like what he describes. So why bother getting upset over what he says? It'd rather listen to him non-defensively. That way I learn something instead of getting exhausted by cheap outrage.
Second, I think he is speaking from a very legitimate place of frustration and anger, and as an agnostic in the public eye he sometimes has to be brash and loud about his ideas because otherwise they don't get listened to. His anger over the influence of religion on public life is grounded in truth and worth hearing. That he insists on framing that outrage in such extreme terms is part of his style, part of the reason why people pay attention to what he says, and I think also his way to speak to the people he really wants to hear him -- other people who feel the way he does but don't feel as free to express themselves. There's a place for that in our public dialogue, and I don't think that it is necessarily a destructive thing. We can hear the truth in what he says without getting pulled in to the rhetorical and stylistic excesses, no matter how sincerely they are presented.
Third, to all those who are saying that you don't need to have known religion from the inside or to have studied it carefully to understand it, and everyone rolling their eyes at the notion that theologians are important ... look, it is actually a good thing, as I think most of us would agree when it comes to other roles in public life, for people to aspire to be somewhat qualified, or at least well informed, when they pontificate about vast segments of the population. That doesn't mean you have to be religious to have a well informed opinion about religion, but it does mean that you shouldn't take for granted that you know what you are talking about because you grew up in an evangelical home or have annoying fundamentalist in-laws, or whathaveyou. And if you are just going off of media depictions of religion, or experiences of religion in one section of the US, you really are drawing generalizations out of narrow experiences so, yes, actually, that lack of experience does make a difference in how closely your opinion corresponds with reality. I prefer less intellectual sloppiness when it comes to talking about people, just like I prefer the reasoning supporting the theory of evolution to that of the intellectually sloppy and disingenuous "theory" of intelligent design.
And since we have of late been on the defensive about the "well educated elitists are baaaaad" stream of American anti-intellectualism, let's not do the same thing with our "oh those theologians with all that silly useless elitist book larnin', who cares about them!" Things like Liberation Theology and Process Theology, or the intersection between the atheistic strand of Existentialism and Christian thought (concepts that are completely lacking in Maher's understanding of contemporary religion) actually have a huge impact on how millions of people experience their faith on the ground on a daily basis. If you don't have some grasp of those concepts (whether you could name them as such or not), you will probably have a very hard time understanding a lot of non-fundamentalist religious beliefs and practices. Dismissing these theologies outright without making any effort to understand them first makes Maher sound intellectually lazy and emotionally reactive. Which is too bad, because he is a very intelligent man with well-placed passion for justice.