From what I can tell, the main reason is the outcome of the following social trends in the early 20th century. 1. Reacting to British Idealism, Russell and Moore found what comes to be known as "Analytic Philosophy" with Wittgenstein playing a major role. Moore and Russell are "infidels" with Russell being very outspoken about it (and given Russell's childhood, who *wouldn't* be an atheist?! It's very sad: a tortured genius.). Wittgenstein, though perhaps a theist of some sort, doesn't want to talk about it. Both men are revered in the new school. 2. Catholics, already having their own systematic tradition, said "Pff" to analytic philosophy. 3. Protestantism splits in the 20's between the "Mainline'ers" and the "Fundamentalists." The latter are suspicious of reason generally, and the former aren't sure they believe anything in the first place (though there are some fantastic exceptions). So as I see it, widespread atheism in academic philosophy is mostly the result of social trends among Christian groups.
What's surprising, and exceptional (and thus evidential) are those cases which buck the trends, the adult converts like PvI, and the fact, indicated in the surveys, that those theists who go into PR manage to keep their belief in an intellectually respectable way. The more I think about it, the more this survey boosts my confidence in theism (though we're still only talking a few percent at most. I'd say between 1-3% boost, but the numbers fluctuate day to day.