A lot of that comes from what happened in Saudi Arabia, with American troops being stationed there in '90, and America being viewed as a non-Islamic occupying force by him. I think the most important long-term strategy is to not repeat the mistake of becoming an occupying force (or, at least, what is viewed as an occupying force, as the way we are viewed is more important than what we are actually doing). An interesting book by Robert Pape (Univ of Chicago Prof) has an analysis of suicide terrorism dating back to 1980, and comes to the conclusion that being viewed as an occupying force leads to terrorism.
Of course, even if we were to pull completely out of the middle east now, we would still have the current generation of terrorists to deal with. However, its absolutely necessary to remove the incentive to become a terrorist in the first place.
I think that the portrayal of suicide terrorists as simply crazy fanatics is a bit silly. Not that these people aren't nutty (attacking civilians, etc), but there is a reason they use the tactics that they do. Suicide terrorism is a logical, strategic weapon. A large majority of suicide attacks since 1980 have NOT been Muslim attacks.
This is one fundamental reason why I disagree with the way the GWOT has been fought. Overthrowing countries like Iraq has the potential to help us short-term (and even in the long-term, by allowing us to work with their intelligence community and government better), but I think the long-term effects of occupying the country are more dangerous than the potential gains from it.