These people replaced their religion with an ideology and did atrocious things. The driving force behind race purification in Germany was the ideology. The driving force behind starving millions in the Ukraine and in China was forced farm collectivation. The force behind millions dead across the world from war was the revolution.
These ideologies were atheist and they were deadly. So the idea that organized religion is unique in people killing each other is silly.
Edit: Where did you get the idea Atheism is a disbelief in anything?!?!?!?!?!?!?! It is a rejection in a god or higher power.
Atheism is the unbelief in a deity or deities.
An Atheist cannot reject something they do not believe exists anymore than you can "reject" the tooth fairy.
Again, the atrocities you cite were not performed in the name of Atheism. They were done by evil men for evil reasons.
Do you believe the Crusades, Dark Ages, Witch Hunts, 9/11, etc. could have come to fruition if the "foot soldiers" or "grunts" who had to do the dirty work did not believe in god? Would there be a "war on terror" today if suicide bombers did not believe 72 virgins awaited them?
EDIT:
To answer the OP's question -- when my parents attempt to bring my children "into the flock" behind my back, evolution deniers want "Intelligent Design" taught in my children's schools, the Catholic church denies people in Africa condoms and spreads falsehoods to discourage their use, people blow themselves and innocents up in the Middle East believing an eternal reward awaits them, ad nauseum ---- THAT is why non-believers get upset.
If those things were to go away and the religious simply practiced their religions privately and without using it as a means to interfere in the lives of others then there would no longer be anything to be upset about.