I've had the "free will" discussion with others recently, and I came to a couple of conclusions:
- it's important to understand the concept of randomness, or Stochasticity, as a recent Radiolab production put it. IMHO we see randomness where there isn't any, where the "model" is instead very-very-very complex.
- similarly, we might think we are exerting "free will", when what we have is the result of many overwhelmingly complex inputs and calculations. Even our perceptions of and questions about "free will" are the result of these processes.

The relevance to atheism comes from the idea that "free will" was given to us by the god, which looks to me like a get-out clause, to explain away non-believers or those who question the established religion. "No, there's no problem with our religion, this guy is just using his god-given 'free will', and will go to hell for it!"