The presense of a bomb is quite plausible. Whatever the case, the official story no longer is beyond criticism. Which is puzzling, since there is no reason to believe that the government didn't honestly think that Flight 93 was about to be crashed into the White House (for example) when they shot the plane down (if they did).
But I don't buy the idea that the government would have any need or reason to "cover up" the presence of a bomb. Other planes have been destroyed by bombs, and the public knows this. All luggage is subject to search, partly due to the danger of bombs--and the public knows this. The fact that there was a bomb on Flight 93 would not by itself have much affect on the public's willingness to fly. This is because it is not obvious to the average airline customer that preventing planes from being blown up by bombs planted in the luggage (or other freight) is at all problematic--and a bomb on Flight 93 would not change the perception. The supposed bomb on Flight 93 would be easily explained away as a one-time fluke, using the same propaganda techniques that are being used so successfully to prevent the public from panicking over other matters.
They also don't want the flying public to know that TWA Flight 800 was taken out by a $7,000 black market shoulder-fired surface-to-air missile because they have no way of defending against that either.