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First, there is no real requirement for for Maher to address the "intellectual" religious community. Borg, Tillich, or whomever else. This is because the VAST majority of Americans in this country have zero interaction with these thinkers. They have read nothing by them and their religious leaders certainly aren't having lectures about the issues they discuss on Sunday morning. Theologians are not influential to the practice of modern religion in America. The most intellectual discussion of religion most believers ever face is what they get in their philosophy 101 class in college. You'd be very surprised how many could not even explain the difference between an Agnostic and Atheist, or give any definition at all of a "nihilist" except that all three are "bad". I highly doubt Maher would have much of an issue with religion if individuals had a wide knowledge of world religions, genuinely questioned their faith, and inevitably admitted that a literal interpretation of scripture is false. Of course, if that actually ever occurred we would have a lot fewer religious people.
Second, I think that Maher and most commenters' point about religion being the cause of wars is that 1) religion leads to non-critical thinking and cultish behavior which encourages war and 2) empirical evidence shows that religion is at least a contributing factor to most wars and human behavior within war environments. The truth is that wars are complex, difficult to define or explain social phenomenon and that any war is the result of myriad factors. One of those factors is almost always religion, as can be seen by the fact that in most wars, the two sides fighting are often from different religious backgrounds and often use markers of religious belief to identify enemies. "moral outrage" at the other side's belief systems is almost always used as a way to justify inhuman treatment of your enemy. That's an empirically verifiable fact.