Al Qai-da has released the most thorough explanation of their position that I've come across: [Link - Special Dispatch Series - No. 388]

It starts off with some pretty obvious and basically true stuff:

"What happened to America is something natural, an expected event for a country that uses terror, arrogant policy, and suppression against the nations and the peoples, and imposes a single method, thought, and way of life, as if the people of the entire world are clerks in its government offices and employed by its commercial companies and institutions."
...
They thought that oppression begets surrender, that repression begets silence, that tyranny only leaves humiliation. Perhaps they also thought that this [oppressive] atmosphere is sufficient to kill man's virility, shatter his will, and uproot his honor. These people erred twice: once when they ignored [the consequences of] treating man with contempt, and again when they were unaware of man's ability to triumph.

But then it goes on to prove that it is no better than the infidel nations it despises, and in fact it's quite worse. They just want to displace Western tyranny and corruption with their own sort of tyranny and corruption. Given a choice, I'll take the Western kind, thank you. Both are worth fighting against but there is certainly a lesser evil here. You should really read this thing. It sounds like it was written by a paranoid lunatic at parts ...and I say this as someone who is against American support of Israel over Palestine, against the multinational corporate corruption and against the rampant political corruption surrounding us all.