Hitler disliked the clergy, not the religion. He sought to reduce the influence of organised religions on society so that he could increase the power of the state. Things get muddled beyond that.
There are plenty of historical revisionists who try to paint Hitler as rabidly anti-christian, but precious little proof. They take his desire to see the christian influence on state matters broken as some sort of evidence that he was planning a purge. But Hitler was above all pragmatic. He didn't seem to care overmuch what people believed so long as they obeyed.
More interestingly, Hitler made constant references to "the almighty" and "the creator". So much so that a great many scholars feel that they went beyond mere pandering to the masses and that he, himself actually believed in a deity. This is typically believed to be the god of Abraham as his mother was Christian and he never seemed to talk about deities plural, only singular.
As for the rest, why people kill absolutely matters. It's what allows us to learn from the atrocities and prevent them in the future. There were no major killings in the past 125 years that can be attributed to killings in the name of atheism. Atheists do not kill others in order to eliminate religious beliefs.
But oh, the hundreds of millions that have been killed in the past 125 years in the name of religion, ethnic hatred or other forms of bigotry and intolerance! Funny how you'd have everyone simply ignore that so you can preach your own bigotry and intolerance.
And yes, atheists are soulless. So are you, by the way. Because souls don't exist. Being soulless, however, is not cognate with being immoral. This can be proven quite simply: there is no god (or gods) so all morality is godless. Whether you are taught your morality through the institution of a church or you come to your morality through some other means, no deity has any part in it because deities do not exist. Cut and dried.
The result of that, of course, is that we must accept that some people are pretty horrible, regardless of their upbringing. Atheist, christian, buddhist, shinto, worshiper of the almighty Kermit the Frog, it doesn't matter. Some people are genetically beyond redemption. Others are genetically on the fence and environmentally sent down the wrong path, and some are perfectly normal then broken by events and ultimately end up beyond hope.
So are there atheists who have done bad things? Sure! But they tend to do those bad things in the name of power or politics. Without a deity to hide behind the part where they're fucking loony tunes and evil as a bag of rancid wiener juice is pretty obvious from the beginning.
But theists are another story. For thousands of years they have bamboozled empire after empire into giving them special dispensation. They swindle and hoodwink billions into belief in something that doesn't exist. Hell, they can't even agree amongst themselves what does and doesn't exist. It's all lies upon bullshit upon scams from top to bottom.
So when one emerges from amidst the theocratic cesspool of irrationality and starts agitating for extra special layers of hatred and bigotry it's pretty hard to separate them from the rest, at least initially. And once you know for sure that you've got bona-fide fucksticks running about, they hide behind the "religious tolerance" laws and cause untold pain and suffering without anyone who is allowed to stop them.
Sometimes it's just harassment and bigoted trolling like Westboro Baptist Church. More often it's really fucked up beyond all accounting shit like Scientology. But every now and again you get an Inquisition or Crusade or Jihad. Then you have Chechnya or Sudan or the entire middle east forever and ever amen.
Religion is nothing but bigotry and hatred protected by law. It's about having everyone obey an unelected set of leaders who tell everyone what to think, believe and do and socially excluding, shunning, excommunicating or even killing those who refuse to bend their will to the crazy trying to use figments of everyone's imagination to obtain power over the masses.
There are lots of shitty reasons people to shitty things to eachother. Almost all of them are about someone's desire for power over others, and the milled masses being too afraid to say "no". But it is damned rare that someone kills is the name of atheism while killing in the name of theism happens all day, every single fucking day.
Religion is a problem. Perhaps the biggest problem humanity has ever faced. We need to grow out of this infancy, and quickly.