The above post raises an excellent point that conflict is often not religious but something else. Most religions in the world are ethnically based; the only exceptions being the missionary religions of Buddhism, Islam and Christianity. Even so, those two have some ethnic favoritism about them with Christianity being favored by Western Europeans, Islam by North Africans and people from the Middle East and Indonesia, and Buddhism by the people of East and South Asia. It is perhaps the ethnic differences rather than the religious differences that have caused the conflict.
Still, conflict often exists between people of the same faith: Protestant vs. Catholic; Sunni vs Shia, etc. Again, the missionary element comes into play. Missionary religions tend to believe that theirs is the exclusive religion and all others are wrong. They are often inclined to fight others who differ with them under the perception that they are fighting for and to protect their religion. It is often misinterpreted as missionary fervor; even though the founders of all these religions spoke against violence. So bottom line, the biggest problem is not the religions, but the people who practice them.
First of all, this depends on the idea that religions really do have the same aim. I think that it is very easy to argue that they do not. For example, it is very easy to argue that the aim of both Christians and Muslims is to bring people to believe in their particular view of God. You can say that they both want to bring people to God, but it is also possible to argue that they only want to bring people to their view of God. In that case, the conflict is not at all hard to understand.
Another way to look at this is to say that the followers of various religions are not really fighting over religion but over something else. Their leaders may use religious rhetoric to motivate people, but the true conflict is not religious. For example, you could argue that the conflict between Arabs and Israelis is not about religion but about ethnicity, land, and power. Religion is just a way of making the conflict look more "moral" and less selfish and greedy.
These are two ways that you could answer your question.