Rape exists in all human cultures to some extent or other.
Can we therefore say that rape is natural?
Probably we can. However being natural does not necessarily make it good or right and I would argue, as an atheist and firm advocate of evolution, that rape is in fact morally wrong and that rapists should be punished by society.
Are humans endowed with sexual urges and are these urges genetic in basis? Certainly, although looking for a "rape gene" is almost certainly a pointless task as a complex interraction of genetics and social experience is almost certainly at play in such cases.
As well as complex sexual urges we also have evolved the intellect and unique ability to empathise with others. This allows us to understand anothers suffering and to appreciate the consequences of our actions on others. This in turn enables us to understand that it is not "right" to inflict on others atrocities that we would hate to be inflicted upon ourselves or those that we love.
Our ability to empathise is what makes us moral animals, is what guides the rules on which societies are formed and is the basis for rape being considered wrong in any civilised society.
That will not stop rape occurring, especially in dehumanising situations such as war, but it does mean we can morally condemn those who commit it regardless of any reference to some sort of natural or evolutionary based argument for it's proliferation.