I know that it really feels like we are free, but even more importantly, if we do not have free will then our lives lose a heck of a lot of meaning. It's a depressing view where we are mere biochemical machines thinking that we choose how we act but where even our very thoughts and desires are determined by mindless chemical interactions. We cannot then assign moral value to anything and even praise or blame for any action whatsoever is entirely misplaced.
After chewing on that for awhile I think most people will not want to live in such a worthless view of life and decide that they believe in free will regardless of what the evidence so far supports. Whether free will exists or not, I don't know, but the point is that in "choosing" free will we demonstrate that the positivist's method is not good enough to build a meaningful philosophy. We find that we must engage in speculation and live as if many unproven things are true. Essentially, even the atheist must have a form of faith.
With such a realization it is apparent that the atheist can no longer claim complete rationality in his views. Does this prove the theist correct? Not at all. But it does serve to hurt the atheist's standing and perhaps provides the justification to begin exploring other meaningful kinds of speculation.