For the theist, and perhaps particularly moreso for the Christian theist, the roots of morality are a rather simple matter: we are made in God's image, and moral intuition and character are etched or instilled into our very essence. In other words, we are the moral agents of God. While we cannot attain the moral perfection of the sinless Jesus Christ, we can be well aware when we are violating the moral purity of God's character. Even if we are not aware of it this is so, how many of us have a "guilty conscience" over something there would be absolutely no rational materialist reason to feel guilty over (i.e., pocketing the extra dollar the cashier gave us; or, not stopping to help the lady change her flat tire in the rain)? For the theist, the reason we feel this way is obvious, we have violated God's perfect moral character. For the atheist, why would they feel a guilty conscience?
While an atheist could be a good and even far better person than a theist, in that they can know the moral law, the atheists have a very difficult time in explaining where the moral law comes from. A matter of knowing (epistemology) is as open and obvious to the atheist as to the theist, but the atheists miserably fail in explaining where the morals come from in the first place (ontology), and in denying the existence in God, the atheist answer to their ontological conundrum are hocus pocus on one hand, and abra cadabra on the other. That is, they either think morality is just there, and that is all there is to it, or somehow we have accumulated moral wisdom over centuries. But still, neither answer provides an adequate answer to the question of origination.
If you spend some time and attempt to conjure up a moral beginning for civilization, a case for moral autonomy, and a justification for human worth, you rack your brain and ultimately come up with the existence of a creator God (i.e., Jefferson, Declaration of Independence).
Briefly, the existence of ethics and a moral center is far better explained, and much less stretched in explanation by the presupposition of a moral God, as opposed to the explanation of an amoral philosophy which posits that human beings became moral characters essentially out of nothing.
This is very brief and to be fair, I didn't do justice to either side's argument (especially the atheist's side), but even if I were to summarize all the accumulative positions of various atheist moralizers, it just wouldn't make very much sense. It amounts to a bunch of educated guys just starting with the incredulous position of no God, instead of admitting that the theistic explanation is much more simple, and coming up with some really whack ideas about the origin of morality bestowed by nothing. Adversaries could argue that theists are starting from the credulous position of a God, but that doesn't refute the point that morality is easily explained by the existence of a moral God as opposed to an amoral nothingness.
A more complete argument from the atheist position is found here, in the essay with a bothersome title "Atheism, Christian Theism, and Rape."