Counterexamples to refute the assertion that the US government cannot keep "big" secrets:
(1) A US bomber accidentally dropped a hydrogen bomb out of an airplane into the dessert near Albuquerque, New Mexico, triggering a conventional but non-nuclear detonation. This happened in 1957 but was kept secret until 1986 -- a span of 29 years. "It was only in 1986 when an Albuquerque newspaper published an account based on military documents recovered through the Freedom of Information Act." (ref: http://www.hkhinc.com/newmexico/albuquerque/doomsday/ )
(2) The British were regularly reading encrypted German messages by around 1940. The codebreaking of the German Enigma machine was one of the greatest secrets of World War 2, and the British shared the knowledge with the Americans. This secret was revealed in 1974--after 34 years--because of two books by key intelligence figures. (ref: http://en.wikipedia.org/wiki/Ultra#Post-war_disclosures )
In both cases, at least dozens of people--but more likely hundreds of people--would have been privy to the secrets. But these two secrets did not leak for 3 decades.
Note: I am not endorsing any 911 conspiracy theories. I am simply showing that the stubborn meme that the US government cannot keep big secrets is incorrect.
a) Monica Lewinsky
b) Watergate
c) CIA Renditions
d) Waterboarding
e) More recently, intimate details of Seal Team Six & the Bin Laden raid.
f) Warrantless Wiretapping
Suffice it to say, the larger the likely public interest - is the more likely that leaks will appear.
If this was an inside job, there are not so many people (especially public people) who were behind it. They just needed to hire some Arabs (through several proxies) and train them to intercept the airplanes. And I'm sure those Arabs didn't know who was really behind it (they were sure it was Osama who could be an agent or a legend). Then make sure the secret services somehow fail to do their job at time X. Then eliminate/threat/silence those people at lower levels who couldn't understand some actions/lack of actions and were suspicious about that.
It isn't so hard for people with sufficient power and money, don't you think?
It's not that I doubt that people would want to (and perhaps have motive) to pull off a stunt like this.
It is the subsequent burying of the evidence and keeping it a secret for so long - something that has attracted more scrutiny than any other terrorist attack in recent history.
Either the gov't is far more sophisticated than we imagine, which I doubt - or the theories are just that. Theories.
I am more inclined to believe the latter.
I'm no demolitions expert nor am I a physics major, so I can't speak as to how structures of that size behave under those conditions - though I'm sure the conspiracies have been thoroughly debunked by now. But that's the thinking.
Personally I'm more inclined to disbelieve a conspiracy theory simply because there's no way our government is competent enough to keep a secret that big for eleven years - across multiple administrations. But who knows - maybe there're better at their jobs than I'm willing to give them credit for.