Let us assume arguendo that theistic ethical critique directed towards materialists and naturalists* is correct: there are no natural, material reasons whatsoever to refrain from murder, genocide, rape, theft, and mopery on the high seas. There are no natural, material reasons whatsoever to be polite, properly tolerant, or respect any rights or obligations towards others.
*not atheists: many atheists are to some extent idealists and dualists; many are not even skeptics.
In which case, there is no more reason to be "good" in the above sense than there is to confess one's supposed "sins", to obtain communion, to spend hours on one's knees giving thanks to the ceiling, to rub blue mud in one's navel, or to offer our children's orifices to the sexual gratification of the priesthood. Certainly any natural materialist would confess there are no good reasons to be "good" in the latter sense.
The argument asserts then that everyone would really be better off if they did not, for example, refrain from casually killing others. But if we really would be better off murdering people right and left, in what sense, then, are atheists inferior to religious believers? Do theists not want people to be better off? If there really is no natural reason not to kill people, then in what sense are theists claiming that the prohibition of murder is not as much a ridiculous superstition as ritual cannibalism? And if the prohibition against murder really is a ridiculous superstition, then it really would be better if we abandoned it.
Of course the theists are trying to have their cake and eat it too: They explicitly reference murder, genocide, torture, etc. (and the lesser virtues of politeness, tolerance, civility, etc.) precisely because there are natural reasons for the relevant moral beliefs. If they did not believe there were natural reasons for these moral standards, they would not bother to use them as examples: it would be equally forceful to say (accurately) that there are no natural, material reasons to eat fish on Friday, tithe to the church, not eat pork, or engage in any of the other arbitrary, meaningless religious strictures (not to mention cruel and oppressive strictures) that do nothing but indicate one's submission to the self-appointed spokesmen of an invisible deity.
Of course there are natural reasons to refrain from murder, etc., there are natural reasons to be (under ordinary circumstances) polite, tolerant and respectful of others. There are abstract reasons, such as reciprocal altruism, as well as causal reason: our biological and social/cultural evolution and our individual upbringing.
It is rational to do something because you want to do it. Indeed it's not only rational, it's the only reason anyone does anything other than submit blindly to the laws of physics.