The above is mostly a summary of www.flight93crash.com but it has one bit that I hadn't heard before. It seems clear that the feds are covering something up here (e.g., ordering civilian air traffic controllers not to talk about what they saw on their scopes) but the big question is... why? Clearly the plane was hijacked, so what are they trying to hide? If they shot it down, why keep that a secret? If there was a bomb on board, why keep that a secret?
The only explanations I can come up with are pretty thin: "they're afraid of public reaction to shooting down commercial planes"; "they like the hero story for propaganda purposes". Those could be the reasons, but they don't seem like very good ones; they could tell the truth about either of those with the proper spin and have it sound totally reasonable.
But (from the above article) here's a really good reason why they might want to hide the truth: maybe they used classified technology to bring the plane down:
Others might say, as they have done about a TWA flight that fell to the sea in 1996 after taking off from New York, that the plane was a victim of electromagnetic interference. In the case of the TWA flight, the argument, put forward in a series of exhaustive articles written in the New York Review of Books by the Harvard academic Elaine Scarry, is that it happened accidentally. However, as Scarry's articles relate, documentation abounds showing that the Air Force and the Pentagon have conducted extensive research on "electronic warfare applications" with the possible capacity intentionally to disrupt the mechanisms of an aeroplane in such a way as to provoke, for example, an uncontrollable dive. Scarry also reports that US Customs aircraft are already equipped with such weaponry; as are some C-130 Air Force transport planes. The FBI has stated that, apart from the enigmatic Falcon business jet, there was a C-130 military cargo plane within 25 miles of the passenger jet when it crashed. According to the Scarry findings, in 1995 the Air Force installed "electronic suites" in at least 28 of its C-130s -- capable, among other things, of emitting lethal jamming signals.