hijacked aircraft used hostages to trade for something.
The WTC attack used a different tactic - using the airplane itself. Up to yesterday, it was reasonable to assume that a hijacking would involving trading the passengers for something (a trip out of the country, someone freed from prison, etc.) Having a small arm and threatening the hijackers did not improve the situation.
Furthermore, we're taking about a pressurized tin can. Small arms tend to punch holes through the can - depressuration and all.
However, I think they're used to be Sky Marshals.