Here's a thing. Atheism, being a negative position, takes no position on morality. That said, a great number of atheists are, more or less, humanists, which derives what I would consider a fairly strong sense of morality (admittedly not a moral code for the lazy) from the ideas that the best thing to do is that which benefits the population the most, and that there are such things as victimless crimes (i.e. crimes that harm only the criminal) that are often best downplayed or ignored.
From this proceeds the idea that the strongest indicator of what is and isn't moral is mutual respect, and from there the idea that informed consent is critical to virtually all social interaction. From that logic, most concisely summed up in the Wiccan Rede and the Golden Rule, and not merely from the arbitrary positions of some people who happen to be godless, comes the idea of "atheist" morality and the idea that rape is wrong.
In more concrete terms, rape violates the personal space and right to self-determination (over one's life and one's body, specifically) of one person and the trust of the community at large. Even if there is no physical injury, the rape victim has still been deprived of the ability to consent, and has been unwillingly exposed to any number of problems from public humiliation and psychiatric distress to lethal sexually-transmitted diseases. Only a particularly dimwitted nihilist could argue that any of this is irrelevant.
And now I feel decidedly dirty having dug this deep, in such a clinical manner, into the reasons why rape is wrong, and I have to go do something.