When we talk about religion most people(I mean, Atheist) thought that it do so much harm to humanity, taking the Crusaders which engendered much violence in the name of Christ ( as their favorite example). What we need to know is that this action is not justified instead it is in serious contradiction with the message of the gospel.
Atheist world does more harm to humanity, say for example 'the holocaust'. We may call it conflict of ideas but the real problem is 'the idea without God, the Creator'. When you omit God you can justify whatever you do and you can make your idea your god as there is no one greater than you.