It started much earlier than that, when the CIA took over Nazi Muslim terrorist networks after WWII, and from that started working with the Muslim Brotherhood in the 1950s. Ian Johnson's _A Mosque In Munich_ is a must-read if you are at all interested in why 9/11 happened:

Privately, President Eisenhower seemed concerned about how to reach the Muslim world. He wrote to his confidant, the Presbyterian church leader Edward Elson, that Islam and the Middle East were always on his mind. “I assure you that I never fail in any communication with Arab leaders, oral or written, to stress the importance of the spiritual factor in our relationships. I have argued that belief in God should create between them and us the common purpose of opposing atheistic communism.” In White House meetings he was more blunt. Speaking with the CIA covert operations czar Frank Wisner and the Joint Chiefs of Staff, Eisenhower said that Arabs should dip into their own religion for inspiration in fighting communism. “The President said he thought we should do everything possible to stress the ‘holy war’ aspect,’ according to a memo outlining the conversation. “Mr. Dulles commented that if the Arabs have a ‘holy war they would want it to be against Israel. The President recalled, however, that [King Ibn] Saud, after his visit here, had called on all Arabs to oppose Communism.” The Operations Coordinating Board — the body set up to imple- ment covert plans by the CIA and other agencies — took up Islam. It had already produced a detailed study of Buddhism and how that religion could be used to further U.S. interests. In 1957, the board established an Ad Hoc Working Group on Islam that included offi- cials from the U.S. Information Agency, the State Department, and the CIA. According to a memo on the groups first meeting, its goal was to take stock of what public and private U.S. organizations were doing in the field of Islam and come up with an “Outline Plan of Operations.’ The plan had two main components, both of which were echoed in CIA actions in Munich. First, the United States would shun traditional Muslims in favor of “reform” groups, like the Muslim Brotherhood. Then, as today, the Brotherhood’s radi- cal political agenda of a return to a mythic state of pure Islam was obfuscated by its members’ use of modern symbols, such as West- ern clothing and rhetoric. “Both the Chairman and the CIA mem- ber felt that with the Islamic world being divided as it is between reactionary and reformist groups, it might be found profitable to place emphasis on programs which would strengthen the reformist groups.” In May, the coordination board passed the inventory and plan of action. Its statements were clear and simple: Islam is a natural ally, communists are exploiting Islam, and Islam affects the balance of power. The paper listed a dozen recommendations for strengthen- ing ties with Islamic organizations, especially those with a strong anticommunist bent. As always, the operations were to be covert. “Programs which are indirect and unattributable are more likely to be effective and will avoid the charge that we are trying to use reli- gion for political purposes,’ the report concluded. “Overt use of Is- lamic organizations for the inculcation of hard-line propaganda is to be avoided”