It is my understanding that commercial flying is less profitable than it once was, which wasn't much better.
As regualtions increased, driven by "bad events", the costs kept climbing in aircraft operations. Add to that the skyrocketing cost of insurance, brought on by an increasingly litigious society. Last, the availability of rock-bottom fares over the internet, which had previously been unknown, drove down revenues.
In short, customers aren't willing to pay enough to keep all of our airlines profitable, and that was true for most operators, even before 9-11. When a situation like this happens, attrition occurs in the industry. Carriers die out, and younger, more cost effective carriers move in. The new cariers have less retirement costs, lower labor costs, and smart young enterpreneur owners. Finally, when enough carriers have restructured or gone out of business, the public has reduced choices, which allows fares to rise to a point of equilibrium. That balance point promises to be lower than many expect.
This particular business cycle has been very hard on aviation, and when it rebounds, there will be several marginally profitable carriers, but it won't be what we all knew it to be in the 90's.