Already do what?
see the difference is that atheists don't share the same beliefs, when someone tells you they're an athiest all that tells you is that they're not a theist. It's as if you told me you're not an athiest, evidently you believe something spiritual but as what those beliefs are I have no idea so it would indeed be unfair to hold you accountable for the crimes committed in the name of Christianity or Islam.
An atheist is "not a theist" as much as a theist is "not an atheist". So yes, when someone tells you that they are a theist, all that tells you is that they are "not an atheist". So according to your own rules, it would indeed be unfair to hold any theist accountable for the crimes that you would say were committed in the name of any religion.
But you're not just a nondenominational theist are you?
I don't think you have a clue what I am.
Not all Nazis were bad people, some believed in a glorious future, some genuinely thought they were making the world a better place, some no doubt thought the sacrifices and atrocities would be worth it in the end, they might even have been right had they not lost the war.
One might make the same argument for the allied countries such as your own. Had the Germans won the war, then you might have been thought of as the evil ones.
But they did lose the war and they were all held accountable for the decisions made by the few because it was their support, their compliance, that allowed those atrocities to occur.
How is religion any different?
1) Religion is a class noun like "language" and "thought".
Nationalsozialismus was the ideology of the Nationalsozialistische Deutsche Arbeiterpartei (NAZI) party in Germany during the 1930s.
It's like asking "how is language any different?"
2) The NAZI party was a political party.
Religions are religions.
AFAIK, politics is not the same as religion.
3) The NAZI party is generally condemned by all but some small pockets of people.
I don't know of any religion that is generally condemned by all but some small pockets of people, except maybe the religions that used to practice human sacrifice, such as the Celtic religion(s) and the South American religion(s) that used to practice human sacrifice.
4) Only a few hundred/thousand people were put on trial for Nazi war crimes. Over 500,000 people were members of the Nazi party. There were more than 50 million people in Germany at the time.
en.wikipedia.org
So clearly, only a few were held accountable for the atrocities done by the Nazis.