The latter problem was addressed, but it is unclear how TSA will keep qualified marshals on the job.
An August 2004 report by the Department of Homeland Security's inspector general found the program experienced several problems.
In 2002, flight marshals were cited for instances of improper flight conduct, lost or stolen equipment including weapons, failed training and sleeping on duty, according to the report.
But the marshal service disputes some of those findings, and marshals say their performance since Sept. 11 has been good.
American Airlines Capt. Denny Breslin, a pilot and a spokesman for the American Airlines pilots' union, said pilots support the marshal service and see the need for more marshals and specially trained, armed pilots.
Breslin said he works closely with marshals on his flights, typically having a briefing with them on the aircraft before passengers board.
"The crew members know they are on board and what to communicate to them," Breslin said.
Breslin said the death of Alpizar, who had been diagnosed with bipolar disorder, is a consequence "nobody wants to occur."
"You can't tell if a guy's lying. You can't tell if he's taking his lithium that day. You don't know if he's a trained terrorist or a goofball, but the results are the same," Breslin said.