The overwhelming reason for the problems in the Middle East is due Israel.
Basically Israel was cut out of Muslim owned lands in 1948 by the UN to create a "homeland" for the Jews (which was done with the best of intentions, as the jews really didn't want to be in Europe after what had happened).
However, Israel promptly rose to being the most powerful nation in the area thanks to help from the U.S. We gave them planes, we gave them ships, and we gave them nukes, and at this current juncture the only country Israel could not defeat in a war is the U.S. Unfortunately, Israel has been very warlike about keeping or even expanding "their" land, which needless to say is a concern to pretty much every country in the area.
Israel has pretty harsh policies towards the Palestinians (such as bulldozing the houses of suicide bombers, even if the remaining tenants were unaware of what their family member was doing), which really does not help relations any with their neighbors. Meanwhile, the U.S. hardly utters a peep about this while constantly harping on other middle eastern countries for human rights abuses.
In order for any kind of peace in the Middle East to happen, we basically have to negotiate a compromise which would allow Israel to continue to exist, ensure the welfare of the Palestinians (and provide mechanisms to prevent abuse by the Israelis), and respect the sovereignty of the other nations in the area.
Unfortunately, the Jewish Right doesn't want this (They believe Israel belongs to the Jews and only the Jews, and assassinated Yitzhak Rabin for negotiating a peace treaty), the Muslim Right (as we call them in the U.S., "terrorists") thinks that Israel shouldn't exist period, and, scariest of all, many elements of the Christian Right (in the U.S., the "Republican Party" j/k

) believe that the Jews must control Israel in order to allow The Rapture and Armageddon to happen.
So there you have it. The reason the Middle East is in such a crisis is solely because of the fundamentalists from the three religions of Abraham refuse to make a compromise. This is why I'm an atheist.
Hopefully Obama will be willing to put his foot down on all three elements. I have my doubts, but at this point I'm grateful for any pleasant suprises.