The FAA and NORAD did indeed have protocols to deal with hijackings in US airspace requiring a military response. Those protocols broke down somewhat on 9/11. A

The FAA and NORAD did indeed have protocols to deal with hijackings in US airspace requiring a military response. Those protocols broke down somewhat on 9/11. A lack of communication between the FAA and the military slowed down the military response to the hijackings. The 9/11 Commission Report is well worth a read.