In Armin Navabi's book, Why There is No God: Simple Responses to 20 Common Arguments for the Existence of God, he has a chapter called "Atheism has killed more people than religion, so it must be wrong."
Navabi's main argument against this is in a section called Atheism Has No Doctrines. He makes some great points, so I'm sharing that section here.
Atheism Has No Doctrines
The violence within Christianity or Islam can often be traced back to the teachings of those religions because it is embedded in the ideology of the religions themselves.
Even though war and violence in the name of God are often motivated by non-religious ambitions, such as political and territorial gain, religions in such cases are often used as an excuse for justifying such acts, disguising their intentions as holy and recruiting armies of people who would not have been willing to risk their lives for purely secular causes.
People throughout history have been martyred and sacrificed in the name of religion, and holy wars have been fought over the tenets of those religions.
The same cannot be said of atheism for the simple fact that atheism is not a religion. Atheism is a lack of belief in deities. It has no governing dogmatic principles, no rule book and no core ideology. Comparing atheism to religion is like comparing apples and oranges.
It's more helpful to compare atheism to theism, which is simply belief in a deity. While some theists also hold fundamentalist beliefs, just believing that some god exists is not enough to cause wars and violence based on the belief alone.
How many wars have been caused by deism? You'd need some additional dogmatic beliefs in order for that to happen.
No one commits mass murder in the name of theism or atheism alone. Additional dogmatic principles are needed to justify such grisly outcomes. In the case of theism, religions like Christianity and Islam provide such dogma, creating convenient excuses.
Secular totalitarian regimes and religion share this dogmatic element: a belief that a set of ideas are true because an authority figure says so and that questioning those ideas can lead to serious or even deadly consequences.
Therefore, it's not reasonable to say that atheism condones or promotes violence or that tyrants have killed in the name of atheism. Such actions or any other action, both good and bad, do not and cannot speak for atheism in general, as no two atheists necessarily hold any of the same beliefs or convictions about the world.
The only thing held in common between all atheists is a lack of belief in deities.
This means that some atheists are undoubtedly unkind, aggressive and violent. It also means that some atheists are kind, friendly and peaceful. Any type of person can be an atheist, just as any type of person can be not interested in golf. Just because some non-golfers are jerks doesn't make not golfing bad any more than atheism can be blamed for the behavior of a handful of atheists.
If you're trying to make a decision about whether you believe in God based on how a certain non-believer you know acts, you're using flawed reasoning.
For the same reason, not all religious people are bad or cruel individuals, yet the practice of violence and war is deeply embedded in many religious ideologies. It is, therefore, best to examine your views about God or other religious beliefs by evaluating the evidence provided for such claims, not based on the behavior of people who do or do not accept it as truth.