As another poster noted would there even have been a 9/11 if passengers had been armed?
The problem with this is that all the passengers could have been equally armed. It's not like the TSA disarmed everyone but the terrorists.
The terrorists had knives, box cutters etc and the other passengers could have had knives, box cutters etc since none of those items were banned at the time. I'm willing to bet that at least one person on each of those planes was also 'armed' in the same sense as we say the terrorists were armed.
You can say, well if a passenger had had a gun it would have been different. Maybe so, but if a passenger could have had a gun then so could a terrorist (since they all boarded as passengers).
The difference came down to what those people chose to do at that moment and its the same now as it was then. In that moment, will passengers standup to the terrorists or wont they.