Yes, there are a lot of these kind of issues in and around the concept of free will, which is why there's a whole branch of philosophy dealing with it. But the point is that free will doesn't require God. You can believe in a perfectly deterministic, godless universe (or fluctuating quantum field universe) and also believe in a compatibalist form of free will.

UPDATE: A brief summary of compatibalism: http://www.rep.routledge.com/article/V014SECT1