They may have been too gentle to kill another humanoid.
Or if they fought back, they may have been massively outnumbered by humans.
Obviously, humans love to kill and wipe out entire species. They may have had an agreement of peace with the neanderthals and then simply lied about it and killed and tortured them all. They may have raped their neanderthal children, which would have led to the gene transfer.
update: I'm sorry if I've offended anyone. Humans don't rape. I take that part back. And humans aren't that violent (except against native americans, maybe, which is pretty minor.)