The difference is that both the farming [read: Islamic] civilization and the foraging [read: American] civilization are complete and self-sufficient systems of property [read: religious] rights. No deal exists that would enable them to coexist and maintain their full sets of property rights. The farmers will have to become foragers, or the Indians will have to become farmers, or else the Indians have to become cocooned in what to the farming world looks like another ranch: a reservation.
Thus it is incorrect to say that property rights exist on the foundation of non-violent cooperation. They do that only within the confines of some civilizations. In other civilizations, property rights are something that is determined in a fight.
Do you think it would be in error to parallel the property rights of the Indians/farmers as argued with the right to freely practice religion between American/al-Qaeda? That is, if we "agree on rules" and duke it out, so long as we play by them the al-Qaeda are justified in defending their culture from "disruption?"
Absolutely -- they can, for example, send us Muslim missionaries (and in fact they do) or ask us to keep our religion completely out, as the Saudis do, -- and the same goes for any other grievance real or imaginary that the militant Islam has voiced. If they don't like American bases in Saudi Arabia they can get the Saudi government to ask us to leave, or they can get Canada ask them to come and set up a training camp in Nova Scotia, whatever. Arafat could demonstrate statesmanship given so many opportunites he was given by the West, and negotiate his way to Palestinian statehood. Those agreed upon rules are internationally recognized norms of conflict resolution, but the militant Islamic civilization organically cannot abide by them and retain its identity.