Has the safety flap surrounding Southwest Airlines rattled you? Have the fears you bury at the bottom of your carry-on bubbled back up to the top of your mind?

That's good. Be afraid. Fear is a frequent flier's best friend.

I've been flying for 30 years, and my head tells me that the system is safe. There are millions of flights and billions of passengers every year, and I can count on one hand the number of fatal crashes blamed on the failure of safety systems in this decade. We're talking Ivory-soap safe: 99 44/100 percent.

But there's always fear in my heart. I remember when one of my flights had to make an emergency landing on a frozen lake in Maine and wonder what would have happened if it had been summer. I'll never forget the day that two of my flights aborted landing just seconds before they would have smashed into aircraft on the runways below. And in my head I always hear my frequent-flying wife's assessment: "I think it's a miracle that planes ever fly."

Yes, it's true that more people die from slipping in their bathtubs than from plane crashes, that flying is the safest form of mass transit, that statistics prove you're at a greater risk of injury in the cab en route to the airport than you are in the skies. Yet every safety scare revives our deep-seated fears about hurtling at 600 miles an hour in a metal tube 35,000 feet above terra firma. And yes, there are reasons that those concerns are valid.

Inspecting Paper, Not Planes
If you're looking for an intellectual rationale for your fear, the Southwest situation is a perfect place to start. The record fine of $10.2 million came only after our safety watchdog, the Federal Aviation Administration, found irregularities in Southwest's reporting regimen. And when Southwest briefly grounded dozens of planes last week, it was because the airline noticed a hiccup in its own paper stream.

The situation reveals an ugly truth about how we monitor airline safety: Generally speaking, the F.A.A. inspects paperwork, not airplanes. The agency doesn't have vast armies of white-coated inspectors who routinely investigate aircraft and maintenance facilities. Instead, it mandates procedures and trusts the airlines to perform the safety checks and required maintenance work. Airlines then file a blizzard of forms testifying to their compliance. If an airline fudges records or F.A.A. bureaucrats have a wink-wink relationship with a carrier's safety executives—something that may have happened in the Southwest case—it's far too easy to hide.

Outsourcing Safety
As if the paper chase weren't chancy enough, most airlines outsource maintenance work to third-party firms. In a frenzy of cost cutting after 9/11, carriers turned to thousands of supposedly certified maintenance facilities around the world. The F.A.A.'s oversight of these firms falls short of accepted standards. How do we know? Calvin Scovel, the inspector general of the Department of Transportation, the F.A.A.'s parent agency, told Congress so last year.

As the amount of outsourcing skyrockets—outside firms now perform about two-thirds of airline maintenance—the F.A.A. is falling further behind. Scovel said that airlines don't have to identify their outside contractors, and some work is being done by shops and mechanics that aren't F.A.A. certified. "Without some form of verification, F.A.A. cannot be assured that air carriers have provided accurate and complete information," Scovel warned.

The Fatigue Factor
Everyone and everything involved with flying—pilots, flight attendants, mechanics, and even the planes themselves—are exhausted. Once again, cost cutting is the culprit. After years of airline budget cuts and downsizing, the surviving flight crews and mechanics work longer hours than ever. Fatigue and jet lag mean that employees aren't operating at peak efficiency. And aircraft that used to fly just a few hours a day now operate for 12 or even 16 hours a day, leaving little ground time for repairs.

The fatigue factor reached a frightening crescendo last month in Hawaii. A Go jet flying the 214-mile route between Honolulu and the Big Island overshot the Hilo airport by 15 miles. Air-traffic controllers were unable to reach the flight crew on the radio for about 25 minutes. The F.A.A.'s suspicion: Both the pilot and the co-pilot were literally asleep at the wheel.

Out-of-Control Air-Traffic Control
The government-operated air-traffic-control system is overworked, understaffed, outdated, and being ripped apart by internal dissent. Endless streams of reports from the Government Accountability Office (Congress' investigative arm) and the National Transportation Safety Board, which investigates accidents, have reached the same conclusion: The F.A.A. has bungled much-needed upgrades of its 1950s-era computers, employs too few controllers, and overworks its staff.

One tragic example is the 2006 Comair flight that killed 49 people when it took off from the wrong runway in Lexington, Kentucky. (Comair is owned by Delta Air Lines.) A subsequent investigation revealed that members of the flight crew had outdated maps and were working on short rest. Why didn’t the air-traffic controllers catch the errors before disaster struck? There was only one controller on duty instead of the required two, and he was working on two hours of sleep.

Meanwhile, it's estimated that controllers are retiring at three times the expected level, because senior staffers—most of whom were hired after President Reagan fired striking workers in 1981—object to a new, unilaterally imposed contract that cuts their pay and imposes a picayune set of work rules.

Does any of this distressing news mean you should cancel your next flight and cower behind your desk? Of course not. But it does mean it's okay to be worried.

As my wife says, flying is a miracle anyway.

The Fine Print...
One more thing to worry about: Pilot pay has been slashed so drastically that airlines can't find qualified candidates to fly commuter aircraft, the entry-level flying job. With pay for commuter flights starting not far above minimum wage (some pilots have left to drive trucks), airlines are hiring pilots with as little as 500 hours of flight experience. That's about half the old minimum requirement.