I found this part quite telling, from the CIA's warning to shrub:

The plotters were among a number of al-Qaida members who have "resided in or traveled to the U.S. for years" and maintain a support structure "that could aid attacks," Bush was told in a briefing paper given to him on Aug. 6, 2001, at his ranch in Texas.

The paper also warned that the FBI had noted domestic activity "consistent with preparations" for airplane hijackings or other attacks - "including recent surveillance of federal buildings in New York."