You are so right! Many atrocities have been commited using god or religion as an excuse. Remember the battles for Jerusalem throuout history... The problem is not religion. The people in power, who lust for more power, just use others people beliefs as a banner for their own agenda so the masses will follow, they hope. It has nothing to do with sepirituallity or religion, because actualy all religions are quite alike in their principles.
Just be patient with those who persecute you with those words. And forgive. But don't forget. As History is one of the great teachers there is!