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You're missing the forest because all you see in front of you is a bunch of trees...
The reason Bill didn't go after voodoo, animists, and other lesser-known religions is precisely the same reason he didn't bother with Hinduism and other Eastern religions...because they don't play as central of a role as Christianity, Judeaism, and Islam do in this country, the U.S. of A...these are probably the numbers 1, 2, and 3 of religion in the U.S. Islam may be a distant 3rd. in regards to practicing adherents in America, but that religion plays such a pivotal role in defining our foreign policy that you cannot ignore it in the U.S.
By going after the extremists, he's trying to make HIS point, the view of agnostics, atheists, and non-believers...that all religion is CRAZY and irrational, when you look at it for what it is. This is something that even folks like O'Hehir, who probably identify with Maher and "get it" better than most, just don't understand about non-believers. We look at this stuff and say "How can a rational human being believe this shit?"...to the point that they let it influence their daily interactions with everyone.
Even O'Hehir tries to be an apologist for organized religion, saying that Maher can't hold a flame to some religious theologian if he has a legitimate discussion with them about the merits of their religion. But for a theologian to try and justify their beliefs, it'll require them to pop out their (insert religious book here), quote lines from said book, then explain how their religioin can help save the human soul, provide comfort to the less fortunate, ensure your salvation in the afterlife, yadiyada...
To non-believers, that's like having The Ronald McDonald clown come and explain to you why your Happy Meal is so delicious, and why you shouldn't feel bad about stopping by your local McDonalds to have a #12 Chicken McNugget meal, supersized...with a diet coke, so you can sort-of stick with your diet. It's not a conversation...it's a sale's pitch.
Non-believers have been squashed in recent years...their voices have NOT been heard, mainly because they have no religion to preach, no people to save (in the holy sense). All Maher is trying to do is to restore some logical balance to this ongoing dialogue about what role religion should play in our daily lives, and how much of it has to be crammed down our throats whether we like it or not.
I for one applaud you, Maher...