In the years of dealing with atheists and their reasons for denying God's existence, the most common one is morality. They don't like how the God of the Bible behaves. I've been told that God is a tyrant, a bully, and that He throws temper tantrums. Not all atheists say these things, but the majority do. They complain about Noah's flood that destroyed countless people. They don't like it that God had Israel to wipe out other nations. They condemn God for permitting plagues and various forms of suffering. They raise objections that if God were truly good that He would not allow people to be raped, or murdered, or starve to death. The list of complaints goes on and on.
However, their complaints are unwarranted for several reasons.
First of all, they are only expressing their opinions, and though they have the right to opinions, opinions don't make anything morally good or bad. Atheist complaints amount to subjective preferences.
Second, in an atheist worldview, there can be no universal moral absolutes that transcend time and culture. For an atheist to say that something "is" wrong is to appeal to universal moral absolute. But how does he justify such a thing in and atheistic worldview where there are no transcendent beings?
Third, they refute themselves. Atheists often appeal to the culture they are in as the standard to judge the morality of a different culture at a different time. They assume that we are more progressed technologically and socially and so it means that our culture in the modern time is superior to ancient cultures. Therefore, they feel they have the right to judge the behavior of God in the ancient culture of Israel.
Fourth, reducing harm is generally the standard atheists appeal to as a moral compass. Anything that deviates from the overall idea of reducing harm is automatically morally bad. But, this is an arbitrary assertion. After all, who said that reducing harm is the right moral standard? If someone says that it is because that is what people want, then that is Argumentum ad populum which is a logical fallacy of appealing to the majority to establish truth.
Jesus said something important for atheists
Mark 2:17, "And hearing this, Jesus said to them, 'It is not those who are healthy who need a physician, but those who are sick; I did not come to call the righteous, but sinners.'"
The atheists don't think they are sick because they think they are morally superior and can stand in judgment over others. They see themselves as morally healthy and not in need of a physician/savior. They are self-righteous. They do not see themselves as sinners because they don't believe in God's law. So, Jesus did not come for them. He came to find those who need a Savior and know they are not righteous.
Atheists who sit in judgment over God are arrogant. They base morality on their own subjective, personal preferences combined with social norms, and from that mix they pronounce moral judgment. Unfortunately, they are blind to their own self-serving, narrow-mindedness and will never find God.
God tells us to the apostle Peter that He is opposed to the proud and gives grace to the humble, (1 Peter 5:5). The atheists are not humble because they see themselves as morally superior to others. Their self-deception prevents them from seeing the truth, and they will pay for it and eternity.