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.
"human beings are sharply marked off from dogs by their capacity to act for reasons that they explicitly take to be moral reasons."
According to them dogs do not have free will but people do. Probably talking about ethics and moral side of "free will" question, not physical or religious. But even there "free will" is just an illusion in your mind.
UPDATE: A brief summary of compatibalism: http://www.rep.routledge.com/article/V014SECT1