Except the showrunners said publicly they intended it as a 9/11 allegory.
I don't know why you guys are arguing, honestly. Ron Moore wasn't exactly quiet about this. It's not that it was meant just as a direct allegory of the 9/11
attacks, either, but the things we dealt with after it, as a culture, like the limits of freedom, dealing with a "hidden" enemy, and things like that. Much of it was thematic rather than direct transposition of events into a fictional universe (though there was some of that.)