It may be due to their past. Alot of these countries have not been stable since they were French or British Colonies. Think Sudan, Algeria, Yemen among others. Even Libya and Afghanistan were under British control at one point.
Alot of these countries hated it and wanted self-governance which they got but they had no idea what they were doing.
You then got populist leaders like the Ayatollahs, Saddam, the Taliban, etc coming into power to fill the void. Really, the only country that came out of this in the best of shape was the UAE. Dubai for all it's wealth has turned out pretty well.
Some of the issues are also religious. You have the Sunni and Shite divide which does not help things any.
I've said it before and I will say it again. The only way that the middle east will resolve their issues are by MAD. They will need to wipe themselves off the map before anything is resolved.