If, hypothetically, the plane took a missle in an engine as the passengers were in a melee with the hijackers, would that make the passengers' actions any less heroic? Personally I don't think the plane was shot down. More likely it broke up in the air as a result of either overly violent maneuvering over the safe maneuvering limits or as a result of hitting Mach 1 in a powered dive. Regardless of whether it was crashed by a passenger, crashed by a hijacker, or shot down, however, the passengers' efforts' heroism remains.
Personally, I certainly do not think it makes them any less heroic, I just think the evidence points to it being shot down(justifiably).