There is a lot of wrong information in this post. First, the Pentagon does NOT site inside P-56 A or B.
Per
http://www.faa.gov/news/news_story.cfm?type=fact_sheet&year=2005&date=121305P-56A & B are areas surrounding the White House and the vice president’s residence.
The only aircraft that are allowed to fly within these prohibited areas are specially authorized flights that are in direct support of the U.S. Secret Service, the Office of the President, or one of several government agencies with missions that require air support within P-56. These prohibited areas have been in effect for about 50 years.
P-56A covers approximately the area west of the Lincoln Memorial (Rock Creek Park) to east of the Capitol (Stanton Square) and between Independence Ave. and K Street up to 18,000 feet.
P-56B covers a small circle of about 1 nautical mile (about 1.2 statute miles) surrounding the Naval Observatory on Massachusetts Ave. up to 18,000 feet.
Also, P-56-A is not 17 miles in all directions. Look at the approach plate into Regan, and P-56 A and B are well delineated:
http://204.108.4.16/d-tpp/0513/00443VDG19.PDFSecond, the Washington ADIZ did not exist until Feb. 2003. Thus, Flight 77 could not have entered the ADIZ.
I'm sure that commercial pilots don't like the approach to Runway 19 at DCA, which is called the "River Approach", because it's not the typical 10 mile stabilized flight path like you have at Atlanta, Dallas or even Dulles. That's because the straight line extension of RWY-19 goes into P-56. However, the River approach isn't terribly difficult.
And even though I don't have personal information to validate whether or not the Pentagon had guided missles protection in it, I really don't think so. Especially in the 1960's, when the threat was seen as ICBMs launched from Russia. When I've seen pictures of guided missle setups, they're usually pretty large, and are located in areas that have clear views of the largest amount of airspace. Which certainly doesn't describe the conditions in the courtyard of the Pentagon. I do seem to recall that the White House security people were outfitted with shoulder launched ground to air misssles after the Cessna crashed inside the fence. These, however, are man portable and look something like the old style bazooka or current RPG. Again, not mounted in a underground box in the Pentagon courtyard.