I hate, just hate (
) having to play devil's advocate here, but who says the passenger manifest is real? If I were a perpetrator in the (assumed) conspiracy, I would just create my own manifest and have coconspirators act as the loved ones of the "people" I created for the list. You've got to assume that the conspiracy involves the highest levels of power in this country, so it theoretically could be done.
I don't think it was and there's lots of physical evidence to the contrary, which is much harder to fake. Add that to the fact that I knew 5 guys killed in the WTC, and there's lots of reason to disbelieve a conspiracy.