Perhaps I am quite late to the party. But I suspect that atheism has such low retention rates because it is, itself, a form of fundamentalism. By which I simply mean that it relies on several unarticulated and dubious assumptions and that it reduces the inexpressible mystery of life to a series of rote formulae. I think that the standard answers of either form leave subsequent generations lass convinced than their converted parents and, because these children have no self-image to confirm, they leave it the way they leave the JWs.
I think that the religious impulse is something like a natural response to life, its mystery and beauty. And I have the feeling that many atheists are attempting to reject those elements in an effort to control our uncontrollable lives. By rejecting mystery, though, an atheist rejects life, really. Viewed this way, it is hardly a surprise that children of atheists must find that they reject it: it is difficult to live so grimly and so at odds with humanity.