Certainly those who fought back are, at least in my opinion. The one flight that was brought down early (forgive me for not remembering which one) stopped short of its intended target because the passengers on board brought it down on an empty field. They attacked the hijackers with boiling cups of tea, forks, knives, and anything else they could find in the kitchen compartment of the plane.
A group of Americans came together to fight a foreign threat in defense of their country and other citizens. I believe that is the very definition of a militia, and why we are all part of it.