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It's perfectly true that there are a lot of sophisticated theologians whose intellectual approach to faith has nothing in common with that of the idiots Maher mocks. But the problem with bringing this up as a defense against Maher's sarcasm is that the idiots outnumber the theologians by a million to one. The religion that most influences the real world is not the gentle faith of the Talmudic scholar or the Vatican philosopher; it's the blind fanaticism of the suicide bomber and the closed-minded ignorance of the creationist.
To be sure, there have been times when a deeper, more thoughtful faith has influenced the world for good -- Gandhi and King are the (ahem) canonical examples. But no matter how much good this sort of faith may do, it is far outweighed by the combination of violence, tribalism, and plain old stupidity we see in the name of God every day.