The 9/11 Commission report describes meticously how FAA and the military have to handle a suspected hijack (p. 18):
If a hijack was confirmed, procedures called for the hijack coordinator ((from FAA)) on duty to contact the Pentagon's National Military Command Center (NMCC) and to ask for a military escort aircraft to follow the flight, report anything unusual, and aid search and rescue in the event of an emergency. The NMCC would then seek approval from the Office of the Secretary of Defense to provide military assistance. If approval was given, the orders would be transmitted down NORAD's chain of command.103
(The reason I highlighted this one sentence will become clear later.)
This is the theory. Now let's take a look how it worked out in the case of Flight 11 (p.19):
At 8:32, the Command Center passed word of a possible hijacking to the Operations Center at FAA headquarters. The duty officer replied that security personnel at headquarters had just begun discussing the apparent hijack on a conference call with the New England regional office. FAA headquarters began to follow the hijack protocol but did not contact the NMCC to request a fighter escort.111
So the information chain within the FAA worked, but the top FAA official didn't pass the info to the military. Why not? A big blunder, handled by the commission with astonishing nonchalance! But wait (p. 37):
Inside the NMCC, the deputy director for operations called for an all-purpose "significant event" conference. It began at 9:29, with a brief recap: two aircraft had struck the World Trade Center, there was a confirmed hijacking of American 11, and Otis fighters had been scrambled. The FAA was asked to provide an update, but the line was silent because the FAA had not been added to the call. A minute later, the deputy director stated that it had just been confirmed that American 11 was still airborne and heading toward D.C. He directed the transition to an air threat conference call. NORAD confirmed that American 11 was airborne and heading toward Washington, relaying the erroneous FAA information already mentioned. The call then ended, at about 9:34.194
So at 9:29, the NMCC is finally aware of the hijacking of flight 11. Obviously it was informed by the FAA in the meantime, but Mr. Kean and his confrčres don't tell us when this happened. And, very strangely, the North Tower was burning since 43 minutes already, allegedly hit by Flight 11!
But this alleged phantom flight 11 is not what I want to talk about. What I find absolutely UNBELIEVABLE is that the NMCC didn't issue a warning to its boss, Mr. Rumsfeld, about a hijacked plane heading toward Washington! Not only that the NMCC deputy director didn't follow the protocol (see my first quote), he also ignored the possibility that the Pentagon itself was a target (the twin towers were burning, after all)!
It still gets better (p. 38):
The NMCC reported a crash into the mall side of the Pentagon and requested that the Secretary of Defense be added to the conference.198
Pardon? The NMCC "requested" to add Rumsfeld to the conference? That's like a firefighter "requesting" to fight a fire! It's the job of the NMCC to establish communication with the Secretary of Defense, they don't even have to call him, being in the same wing of the Pentagon they just have to walk some yards and knock on his door!
Questions:
Why didn't the FAA headquarters pass the hijack info at once to the NMCC, as requested by the protocol? Or did they?
Why didn't the NMCC deputy director at once seek approval from the Office of the Secretary of Defense to provide military assistance, as requested by the protocol? Or did he?
Why was Mr. Rumsfeld still doing phone calls in his office when a hijacked plane was approaching and threatening Washington? 
