I have not seen a good explanation on this from Americans, who usually peddle the brainless "they hate our freedom" line. Lemmygrad is also sorely lacking any good discussions on this topic.
The U.S. funded the mujahideen to drain Soviet resources in Afghanistan. This makes it rather strange that after the Soviet Union collapsed, Al-Qaeda (one of the factions in the mujahideen) would turn around and bite the hand that fed them.
Was Al-Qaeda dissatisfied with some aspect of U.S. treatment toward them and expected the 9/11 attacks to change that? Or did the U.S. and Israel tacitly allow or even encourage the attacks to provide an excuse to dominate the Middle East?
I would love more sources and reading on this that aren't just pro-US-empire propaganda!