The question is not whether an atheist might have good reason to behave in a moral way. There are many incentives for him to do so. Society might punish him legally or informally for behaving badly. His friends and family members might disapprove. He might suffer physical or financial consequences for doing certain kinds of things. He might even feel bad inside, suffering guilt for doing bad things. But none of those things can really answer the question of whether something is right or wrong. It only tells us if certain actions may have good or bad consequences.
It is in fact perfectly consistent for me to desire not to be harmed myself, while being indifferent to the harm of others or even causing that harm. That can be adequately supported by my desire to avoid suffering myself because I find that suffering unpleasant or a threat to my survival, a principle that does not extend to the suffering of others since that suffering does not bother me. In fact, if my welfare can be enhanced by causing the suffering of others, then there is no rational reason for me to refrain from causing that suffering.
This is just one example of course of how to defend morality in an atheistic worldview. In fact, popular opinion or cultural standards as the basis of morality is the more common argument that I have heard, though it’s an argument that is obviously flawed. If popular opinion defines morality then truly there is no morality, since virtually any kind of terrible crime has been approved of on a popular level at one time or another. Basing morality on cultural standards is essentially surrendering the argument and admitting that there are no moral standards.
If popular opinion or cultural standards were the basis of morality, then in fact it would be immoral to ever agitate for social change, since by definition such agitation would be contrary to popular opinion. If your cause was already accepted by the majority of your culture there would be no reason to agitate for it. Thus, those who agitated for an end to slavery, for voting rights for women, or for an end to child labor were all acting immorally since all of those things were approved by majorities at one point.
Often, atheists will appeal to evolutionary principles. They say we evolve empathy and a desire for social cooperation because those things give us a survival advantage. Without going into the whole argument for and against evolution, consider- if our morality is simply based on evolved traits, then it still can’t be properly called right and wrong, but just what humans do to survive. Humans also often resort to murder and enslavement to improve their survival and welfare. Is that an evolved trait as well? If not, why not? And if so, why is it more moral for me to live by one evolved trait (empathy) and not another (cruelty)? Further, if a man decides to resist his natural empathy and act cruelly to others without regard to the suffering he causes, on what grounds can the atheist say he is behaving immorally? Perhaps he is evolving further, and developing to a greater degree his natural trait of cruelty, and leaving behind his more primitive empathy. If you think empathy is a superior and more sophisticated trait than cruelty, you need to have some principle to base that on. If it’s your opinion that empathy leads to greater survival of the species than cruelty, that is just an opinion, and it’s only a matter of opinion and no cause for moral outrage. Some people might come to a different conclusion about what will benefit their survival and welfare, and you’d have no reason to protest on any moral ground.
The Roman Empire, for example, existed for a thousand years, and the people who ran it had lives of great luxury and ease for the most part. That empire was based on slavery. Slavery was very good for the people who lived at the top. The few slave revolts that happened were always crushed and were never any threat to the survival of the Empire. Eventually the empire fell, but only after a thousand years, and the countless upper-class people whose positions were made possible by slavery never paid any price for their exploitation and abuse of millions of people. Were they immoral to do so? On what grounds?
I certainly prefer kindness to cruelty. I even prefer atheists to be kind as opposed to being cruel, since that is likely to work out better for me. And I know many atheists prefer kindness over cruelty. But there are a great many people in this world, both atheist and theist, who are usually cruel and not kind. We do not say simply that they are what they are, or even stop at taking steps to protect ourselves from them. We react in horror and outrage when innocents are hurt, when men are robbed of their property or the result of their labor, when people say one thing and do another. We react with moral outrage to those things. Yet the atheist’s philosophy offers him no reason for such horror. The truth is that there is an absolute standard, given to us by a Lawgiver, who embedded that standard in our hearts to point us to Himself, for He created us in His image. This is why it is wrong to hurt others, because to do so is an offense to the God that made the other and also made me. The atheist has this moral sense within him regardless of what he claims to believe, and this is why he spends so much time and effort trying to construct moral systems on a foundation of sand, in order to justify the existence of moral beliefs he holds while he flouts whichever ones he finds unpleasant or inconvenient. He knows he is moral, but he wants to define that morality himself, leaving himself free to do as he wishes while still defining himself as a moral person.