Religion is not the root, it is just a tool that is used to create the usual "us-they" opposition, and in its absence there are plenty of other ways to create the same opposition, like "patriotism" and so on. In fact you yourself just created such an opposition, "it's all because of those religious people" and it is already the top comment, showing how eager people are to blame some "they" for all the evil.

That is not to say that particular religious beliefs can not be harmful, but there are plenty of religions and in most of them hatred is not part of the doctrine or ritual unless abuse is made by people in power who would otherwise use any other set of outlooks for the same purpose. There are in fact religions that do not involve "imaginary friends" and interfere little with modern scientific outlook. It could be good to think a bit why religion appeared naturally in different places of the world independently, what psychical needs it fulfills and is there any other way those can be fulfilled. It is a complex and interesting topic, Dawkins-style atheism leads to a "there is no evidence for god so we can just forget about religion" type of stance which makes most "rational" people nowadays not understand the first thing about religion and its role.