To protect the nation's air travelers, federal air marshals deployed after the 2001 terrorist attacks try to travel incognito, often in pairs, and choose flights identified with the potential to fall under threat.

And they almost always fly first class—something some airlines would like to change. With cockpit doors fortified and a history of attackers choosing coach seats, some airline executives and security experts question whether the first-class practice is really necessary—or even a good idea. It could weaken security by isolating marshals or making them easier for terrorists to identify, airline executives say.

With more threats in the coach cabin now, first-class clustering may not make as much security sense. Security experts say bombers are a bigger threat today than knife-wielding attackers trying to get through secure cockpit doors, and Transportation Security Administration checkpoints are heavily focused on explosives, whether hidden in shoes, liquids or under clothes. Some believe bombers try to target areas over the wing—a structurally critical location and also the site of fuel storage—to cause the most damage to the aircraft.

Airline CEOs met recently with TSA administrator John Pistole and officials from the Federal Air Marshal Service requesting the TSA to reconsider the placement of marshals based on current security threats.

"Our concern is far less revenue and more that we have defenses appropriate to the threat," said James May, chief executive of the Air Transport Association, the airline industry's lobbying group. "We think there needs to be an even distribution, particularly when we have multiple agents on board."