I understand what you are saying.
But remember that there were four hijackers with box-cutters, perhaps each with the cutter at the throat of an innocent.
Against one person with a 17 round magazine in a Glock, they would have to mount a suicidal charge at the person with the gun. With even a small advantage of surprise, the odds shift to the armed passenger. If just two of the four hijackers failed to mount an immediate charge of the armed passenger, then the odds shift dramatically, I think. If the passenger ambushes at least one hijacker with a surprise head shot at close range, then there are only three men with box-cutters to fight.
If given the choice between being a single person with 17 rounds to fire versus two people with box-cutters, I choose the gun. There are circumstances where the man with the gun can lose, but there are also many dozens of passengers who can take advantage of the confusion to get in their licks.
Terrorists will never again find docile passengers.