There is a set of procedures for responding to hijackings. In particular, these procedures were changed on June 1, 2001 while Rumsfeld was in power as our Secretary of Defense, in a document called: "CHAIRMAN OF THE JOINT CHIEFS OF STAFF INSTRUCTION, J-3 CJCSI 3610.01A"
(www.dtic.mil/doctrine/jel/cjcsd/cjcsi/3610... )

"AIRCRAFT PIRACY (HIJACKING) AND DESTRUCTION OF DERELICT AIRBORNE OBJECTS"
These are the standing orders to the military as to how to respond to hijackings over United States territory. The June 1 '01 document deliberately changed the existing policies. Previous directives were issued in 1997, 1986 and before.

http://anderson.ath.cx:8000/911/pen09.html