Yeah, this won't be easily resolved here. The previous post did a nice job in explaining the issues. The primary conflict in the Middle East has many roots to it. Yet, I would say that the presence of American support is now playing an even larger role in the region. There is a great deal of resentment towards American involvement and support in the region. Many of the Arab leaders believe that American support of Israel has become an almost "blank check," in which they can do anything and act in any way without risk of international sanction or rebuke. This includes the establishment of settlements in the disputed territories. These leaders feel that American pressure has not been brought enough to bear on Israel. Accurate or not, this is a perception that is either felt or has been manipulated towards the people of the area, causing greater consternation and frustration.
There are many different conflicts in the Middle East, so I am going to assume you mean the one between the Israelis and Palestinians. Just keep in mind there are also conflicts in Iraq, Lebanon and Iran as well.
Most people think the fighting over there is about religion, but that is only part of it, the main conflict is about land. Palestinians are Arab peoples who live/lived in the State of Palestine. Palestine became Israel in 1948 when the United Nations voted to create a Jewish state after the Holocaust. Palestinians believe that land was stolen from them, and want it back. Many refuse to recognize that Israel is a country at all.
Israelis, on the other hand, believe just as the Palestinians that the land is holy and sacred to their religion. They believe God has given it to them just as He did to ancient Israel. They believe they should be able to do whatever is necessary to protect themselves from another Holocaust. Both sides claim Jerusalem and the Tomb of the Patriarchs (where the prophet Abraham is buried) as their own.
Palestinians who live in Israel or Israeli controlled land like the West Bank and Gaza believe they are persecuted for who they are, just like the Jews were in Europe during World War II. They want full and equal citizenship, and the right to return to the land they originally owned before 1948.