I'll admit my instant gut reaction (nothing more) on Sep. 11 was that UA93 had been shot down. Although I do not propose it actually happened, I have not dismissed the possibility completely.
I do disagree that it would have immediately been made public. The US was reeling from the shocking events, and the administration was doing a credible impression of decapitated poultry. To release news of that sort would have been even more devastating. They would have waited a few days until sure that public opinion would have supported it (remember the polls right after the shootdown policy was announced ?). But subsequent revelations of the passengers' heroics, which were not known at the time any orders would have been given, mean that any such admission is now totally unpalatable.
The 'explosion and smoke' reported via cellphone has still not been explained IMO. This would be consistent with a sidewinder hit, ground eyewitness reports not withstanding. And an air-to-air missile would be unlikely to cause the instant disintegration of a 757 (cf. KE007).
As someone else pointed out, if the F-16 jock didn't shoot it down then I would have expected to see him/her placed very much in the public eye - press conferences, interviews etc.
This kind of cover-up would be much easier to achieve than say TW800* or the Vincennes, only a very few people in the loop. I don't rule it out yet, but hope one day I can.
(* an example, I'm not proposing TW800 was friendly fire)