Part of the problem is defining what "morally good" means. Perhaps atheists are more likely to act on thier homosexualality or have multiple (consenting) sexual partners. I would argue that this does not affect whether or not they're "morally good" people, but I'm sure many theists would disagree.
I think in the end, though, it really boils down to the well known quote (too lazy to look up the source...) that goes something like: "there will always be good people doing good things and bad people doing bad things, but for good people to do bad things - that takes religion." When you've got a god telling you to do evil things, even an otherwise moral person may give in. When someone is their own highest moral authority, at least good people will always do good things.