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The truth is, quite frankly, my question is, why do you think they are so mad at us? I believe that is 100% foreign policy related, if not let me know... You can give links if you're otherwise forced to retype.  >>
Okay, i can work with that question.  In the broader sense, i would argue that it's not really that important to understand why they're mad at us.  In some ways,  giving what grieves them the dignity of a name and calling it a "reason" for them to hate us enough to commit an act of mass murder like what occurred on 9-11 is somewhat spurious.  In my view, even a valid and just grievance becomes suspect at best when coupled with an innapropriate response/action (and calling 9-11 an "inappropriate act" is a euphemism to the point of absurdity).  For example, is it important for a parent to understand the motivation for a child who thows a temper tantrum, and attempt to negotiate with him, or is the better approach to simply proceed to the spanking? 
But to answer your question, the Islamic extremeists (hereafter, "Islamicists" for brevity) have,  in their own minds at least, legitimate gripes.  That's not to say that they are valid to anyone but them, but they can be identified and qualified.  Many of them have already been noted and addressed here, but here's a short list:
1.  Islamicists resent the West in general, and the U.S. in particular, for having eclipsed their civilization and its glory days of 1000 years ago.  They pine for the days when the peoples of Islam and the Caliphs were the most advanced on earth, and envy the West and the U.S. for having assumed that position in their stead.
2.  Islamicists have been intellectually, socially, and culturally stagnant for nearly as long.  The Arab world and Islam (with the sole exception of Turkey) pointedly rejected the Enlightenment and modern ideals of Locke, Voltaire, and such, instead choosing to turn inwardly like the Chinese of centuries ago.  
3.  Arab nations and other Islamic nations have not developed socially, culturally, or intellectually to the point of being able to have a population of educated, sophisticated, and skeptical citizens.   Despotism, enforced by thousand year old religious dogma, have conspired to render their populations poor, malleable to be controlled in their opinions by dictatorial and cult of personality dominated "news" media, and mercuric in their opinions. 
4.  Perhaps most importantly at all,  Islamicists seem to have an utter inability to conduct honest self-assessment and criticism, rather relying on blaming others for their failures, be it Israel, the U.S., or whatever other strawman is convienent.  
Essentially, the "reason" that Islamicists are mad at us, is because in the U.S., they see a reflection of their own impotence and the bankruptcy of their belief system.  The culture of the West is simply more advanced and superior to their own in nearly every respect, and this causes what is called in psychology "cognitive dissonance."   Essentially, while they fundamentally understand that the way of Western civilization has triumphed over their fundamental, religiously-based notions of what civilization should be (essentially, a world-wide Muslim theocracy), and they are mentally incapable of coming to grips with that fact in their conscious minds.  Dissonance grown unchecked leads them down the same path to madness and evil that the Nazis took.
Okay, that's my brief take on why the Islamicists hate us.  If you wanted  to ask any more specific questions on specific U.S. foreign policy questions, i'd be glad to give them a shot.   
