We recently watched Syriana, a good but very confusing film, but we were able to take a few ideas away from the movie.
One of the problems in the Middle East and Islam isn't only religion in itself, it's the lack of economic opportunity for the people in many Middle Eastern nations. Seeing the billions/trillions of dollars that can be made in oil, many leaders years ago sold their people down the river in the name of oil. This is probably why in places like Jordan and Israel religious extremism isn't as 'ripe'. These countries have been forced to create a more diverse economy (with a degree of success). Meanwhile, in places like Iran and Saudi Arabia, oil so dominates and these economies that there is little investment into other sectors or areas of the economy. There are only so many jobs that oil can provide and on top of that many of them are occupied by foreigners. The lack of other industries and options leads to many to extremism - in this case religious fanaticism. Just take a look at those who were part of the 9/11 plot - most of them were Saudi Arabian (as is bin Laden) and the remaining few were from the UAE. This isn't a coincidence. The best policy the US could take in the Middle East is to invest in developing dynamic and diverse economies that aren't completely based upon oil.
Also it's easy to see the parallel to this in Africa were we, the West, exploits the natural resources (diamonds, gold, oil, etc) creating economies of havenots. In Africa this has lead to far too many civil wars.
The CIA and the US government will do whatever they can to put the governments that are most friendly to the US in place. I think this comes as no surprise. How successful this policy has been can be debated... it's mos def more gray than black and white. There are pros and cons to such policy.
Big Oil controls this country, they may not run it directly, but they have a lot of people's ear and the corruption is ripe. There is a reason why Big Oil always seems to get the biggest and best tax breaks.