In order to make a massive selling movie about the War on Terror you have to make the 911 attacks just one part of it.
I think people saw Flight 93 as too much of a documentary, when what the US public wants is a much better done version of Pearl Harbor, where you deal with the lead up to war, the attack, and the response and do it from the eyes of people the audience gets to know.
The problem is that we can't make that type of film yet, because we're not finished with the war. In fact, we've just started, IMHO.
United 93 was a documentary, in a sense, and it documented exactly how crazy and vicious our enemy is.