It is true that religion is but one thing among many that are used to define "the other" in order to justify violence and any number of other injustices. Race, language, diet, all manner of cultural differences, and even gender have always been thrown up as reasons to treat "the other" differently. Religion however, is unique among these, in that it invokes (alleges) Divine authority, letting out any possibility of considering otherwise. You either believe that yours are the chosen people and what you do to "the other" is not only justified but a matter of God's will, or you don't. Failing to recognize that unique thing about religion is to ignore history, and reason, for history (not to mention current events) is littered with examples.
I can hear it now, "But religion didn't actually cause..." this or that act of violence. While that is true, it's also true that race, ethnicity, gender, culture, geography, etc. don't cause violence. Those things, and religion, are things without their own will. It is only we mortals who then use those things to justify our (usually selfish) actions, and it is only religion that can be used to absolve our psyche's completely by allowing us the illusion of shifting that will to some Divine authority. Add in the promise of "salvation", rivers of milk, or dozens of virgins, and you have still more reason to just go with the program.
If you're thinking that all sounds like "atheist talk", you're right. Personally, I believe that the atheists are wrong about the Divine, and I find their refusal to admit that there is no more proof for their beliefs (in nothing) than those of any other believer in the world to be annoying as hell, but they are spot-on in their recognition that an enlightened society should never allow religion to justify discrimination or violence.