It is interesting that many religions have more ideals and ethical viewpoints in common than doctrine to separate them. It would therefore be logical to assume that those who follow religious principles would follow the ethic of love an tolerance towards other religious people. This, however, is not the case.
Indeed, for all the millennia of human existence, conflicts have been based on religious differences rather than similarities. Extreme examples are murder and torture committed in the almost crazed drive to "save" the souls of "non-believers."
I believe the answer to the apparently illogical nature of this phenomenon can be found in the dichotomy between general religious ethics and specific religious doctrine. While most religions, for example, actively advocate the ethic of love towards all living creatures, each religion also has its own specific doctrine. Those who pride themselves on their faith often give precedence to differences in doctrine rather than similarity in ethics. Hence, conflict arises, because each religion believes that its doctrine is the ultimate truth. Even within single religions, such as Christianity, various different doctrines are held by different church denominations, which also tend to lead to conflict among Christians.
Hence, as long as specific doctrines differ within belief systems and different religions, there will be fertile grounds for conflict. This is the nature of humanity. Despite any ethic towards the contrary, it is as if we tend towards disagreement rather than basing our interactions on fundamental religious ethics such as love and fraternity.