I've found many intelligent atheists, and I'm sure that there are rational intellectuals out there who disagree with LW. But where are they?

As far as I know, most criticism of LW focuses on its taking certain strange problems seriously, not on atheism. LW has an unusual focus on Pascal-like problems, on artificial intelligence, on acausal trade, on cryonics and death in general, and on Newcomb's Problem. Many of these focuses result in beliefs that other rationalist communities consider "strange." There is also some criticism of Eliezer's position on quantum mechanics, but I'm not familiar enough with that issue to comment on it.