Religions are not "just religions"; they are cultures as well. Just try moving somewhere that people do not have the same religion as you, and you will soon discover how they differ from you in many, many perspectives. Because religions ingrain a certain cultural behavior and beliefs into people, there are conflicts among people since each group feels it is in the right, or are encouraged to perceive others as "the enemy."
Often religion is intertwined with other motives, as well. Religion is seldom the only explanation for conflicts, there are usually economic, demographic, political, and other factors at work that either exacerbate religious differences or are exacerbated by them. So while I agree that religious extremism is a destructive force, I would argue that it cannot be understood in isolation.
Religion is religion. What it all comes down to is that we all worship the same being, just in different ways . . . so what's the rub? We ought to allow all men the right to worship who, how, or what they may and others should allow us the same priviledge. Unfortunately, most wars are fought for four main reasons: money, land, power, and religion. It's really a sad, sad thing!
Family and tradition are a big part of how people identify themselves in the world. People want to feel accepted and to belong to someone or something--and this extends to non-religious things like businesses, sports teams and the like. Why do sports fans get in heated fights outside in the parking lots at game time? It's because they are loyal to their teams to the point of fighting. This is true with anything that humans attach themselves to. Rival gangs get upset if they see the wrong color approach them! It is definitely a human flaw to tie ourselves to certain groups to the point of fanaticism or extremism. I think that true worshippers of any religion do not engage in extremism to gain power and control over others. The true worshippers are those who are peaceful and live what their religion teaches rather than judging others who aren't in it.
I think it's the same reason that some people are conservative and some are liberal. People are simply different. There's not a lot of reason to expect us to believe the same things or have the same values. You can have people from the same family who have very different views on religion so I really think it's to some extent born into our personalities.
My thoughts on religion is that it is something which many who are involved in religion tend to be staunch about. A person's religious beliefs are something he or she takes very seriously. That said, the religion chosen attracted them for a reason (same ideology). Therefore, any religion which speaks against the person's thoughts would not seem right to them.
On the whole, there are not too many things which people can hold tightly to anymore (politics and religion aside). Therefore, people tend to protect the ideas which bring them closer to other groups and separate them at the same time.