We have what I guess can be considered an admission in the form of an approved editorial in the US' New York Times:
As the world ponders the fate of Egypt after Hosni Mubarak, Americans should ponder this: It’s quite possible that if Mubarak had not ruled Egypt as a dictator for the last 30 years, the World Trade Center would still be standing.Further along in the article, we see the typical contortions the US policy class makes to avoid using the word "Israel" in describing US motivations in the region.
These sound like good reasons to welcome Mubarak’s potential overthrow, and the end to America’s decades-long entanglement with his drab, repressive regime. Unfortunately, Middle Eastern politics is never quite that easy. The United States supported Mubarak for so long because of two interrelated fears: the fear of another Khomeini and the fear of another Nasser. Both anxieties remain entirely legitimate today.The United States has one fundamental dispute with Khomeini and one fundamental dispute with Nasser, and they are the same dispute. No non-Jewish population in the greater Middle East believes Israel is a legitimate state. Khomeini's people did not believe Israel is a legitimate state. Nasser's people did not believe Israel is a legitimate state. Mubarak's people do not believe Israel is a legitimate state - so keeping him in power requires the policies that led Egyptians to organize terrorist attacks on the United States.
But for that dispute, there is not reason an independent Egypt or Iran with foreign policies consistent with the sensibilities of their own people, whether ruled by Khomeini, Nasser or any of either's successors would have difficulty maintaining good relations with the United States.