Atrocities committed by those who think they're doing it for; God, the greater good, the betterment of society, for saving their victims souls from damnation and so and so? Those ones you mean?
For example, you really think those carrying out the Inquisition thought themselves evil?
VERY few people commit these atrocities because they want to be evil. They're doing it for what they believe are good reasons.
It's not the bad or evil people that make me wary. You can see them coming and prepare. It's those who cloak themselves in the shroud of idealism that lull you into a state of stupor and cause us to surrender our individual critical faculties that you need to be really wary of.
The third root of evil is idealism.
When people firmly believe they are on the side of good, they often feel justified in using strong measures against the forces that oppose them. Noble ends are seen as justifying violent means. Specifically, idealism seems to be too rigidly attached to a desire to have the world just automatically work a certain way without considering how the world actually works, the means by which we achieve specific goals, that concrete effort is required, or that it takes time.