The relationship between religion and morality is complicated(--duh). There are a couple of issues that critics of religion regularly cite:
 Commonly, we make the assumption that morality simply emerges out of religion. That recreates the Euthyphro dilemma: do we do that which is just because that's what God commands, or does God comnand our doing of the just because the just is what is just, purely and simply?
 Moral codes embedded within the self-understandings of religious communities don't seem to meet the ideals of human nature that those communities (from our modernist point of view, at least) promise. There are outstanding examples of flagrantly bad behavior by religious adherents, and flagrantly bad behavior attributed by religious adherents to their deities.
I'm not completely certain that I've seen this complex of issues dealt with lately in a systematic and satisfactory manner addressed to a secular audience--without an air of superiority or a polemical agenda of one sort or another. For me, this discussion could constitute the basis of a "proof"--in the philosophic sense--or moral argument toward the reasonableness of religious faith, assuming that truth is truth in whatever context it may be seen to abide.
See the discussion here, for example: