Without getting into too much detail in the debate between holycanoli (welcome, by the way, if belatedly) and gumboot, I have to weigh in on the subject with my experiences. Gumboot is entirely correct in every post of his, in my humble opinion, holy; the plain fact of the matter is, this attack was completely unprecedented in many ways. I work in the United States Intelligence Community; I am also a reserve Army officer, MOS 35D, or All Source Intelligence officer. In the year or so since I've begun working for the private company I work for who does contracting for the IC, I have brought the question of pre-knowledge of 9/11 up to nearly every intelligence professional I've met, and all of them have said the same thing; looking back, they can see the red flags and spot the links that they missed before, but PRIOR to 9/11, we assumed, erroneously I might add, that no one would attempt to again attack us on our own soil SUCCESSFULLY. Given that the last successful attack from an outside source (and by successful I mean caused the loss of dozens of lives and had a PROFOUND effect on policies and procedures) was Pearl Harbor, and more than fifty years had passed since then, can you blame us for becoming complacent? It's human nature to, in essence, forget that these things happen, especially if there is a long stretch of time between instances. I call this theory (with thanks to TAM, who I believe coined the term) LIHOIA, or Let It Happen Out of Ignorance and Arrogance.
I've seen you mention the 45 minute time frame on several occasions, but as gumboot stated once, that timeframe is, in fact, erroneous in that the FAA did not inform the military (whom, I might add, did NOT have access to the radar coverage the FAA did; their radar was focused outward, not inward) until approximately 16 minutes before flight 77 struck the Pentagon that it was hijacked. The second that word came down, fighters from Langley AFB were scrambled, but as (once again) gumboot stated, the average time from scramble orders being received to the planes getting in the air is around fifteen minutes.
That being said, I can understand your point, I think. Please correct me if I'm making the wrong interpretation, but you are saying that there should have been preventative measures taken immediately after flight 175 struck the second tower, in the form of a CAP being put into place over Washington, yes? I'm not so positive about the CAP portion of that, but I do feel that measures should have been taken more quickly, such as evacuating all potential target buildings nationwide (which would naturally include the Pentagon, the Capitol, the White House, etc) as quickly as was feasible. If that had occurred, we could have had a couple hundred less casualties, perhaps, but I'm not sure why you think a CAP over Washington would have been a deterrent. As several people here have stated, it would require a humongously desperate situation for the military to order a civilian aircraft to be shot down, especially if it were over a huge metropolis area like DC and the surrounding towns. The debris raining down would likely have killed more people than WERE killed in the Pentagon and would have had the added effect of having a giant hue and outcry against the government and the military for making that decision.
As for who is to blame in terms of the government, I'm of the opinion it has been established already, and I'm not sure what good a full on court martial or inquest would do, as there were so many involved. You've got the analysts, their supervisors, the military, and at least two branches of the government that all bear some measure of blame for allowing 9/11 to occur. I'm of the opinion that bearing the responsibility for nearly three thousand deaths that COULD have been prevented is punishment enough, and now efforts should be turned to finding what was wrong with the system and fixing it. The position of the Director of National Intelligence was created in response to the 9/11 attacks, and Director McConnell is making every effort to put all of the recommendations of the 9/11 commission into place. The Transportation Security Administration was formed in response to the attacks, and having worked with them temporarily on a project for my company, I can tell you they are making every effort to fix the holes in transportation (which includes aviation) security. The intel agencies are now making every attempt to work together and to share their information so as to avoid the circumstances that could lead to one agency having part of the information and another having the other part, and neither agency knowing that the remainder of the puzzle is in the other agency. Ultimately, in my considered opinion, the blame game does no one any good; it's better to focus on what we now know was wrong with our system and fix it.
My two cents. Oh, and a belated welcome to the other new folks as well.