I always thought it was crazy to make the cockpits impregnable for the very reason you mention.
Also, a year or so before 9/11 there was an Egyptian passenger plane that did a nosedive into the ocean right off the coast of New York, with the pilot forcing the plane into the ocean. Some theorized that the pilot was supposed to crash into a NYC target, but instead, forced his plane into the ocean.
In our country, almost every airport calls itself an "International" Airport, accepting flights that originate from foreign countries. Some of these airports are pretty deep inside our borders and the direct flights from overseas to these airports pass over vast areas of our country.
These flights come in on airlines from Egypt and Pakistan, and it worries me that a fanatic pilot could kill his cockpit crew (and while safely behind his impregnable cockpit door) pilot his plane into a nuclear or chemical plant.
Actually, on the flight you're referring to, the pilot committed suicide after knifing his co-pilot to prevent him from interfering. It was later determined that the man's social life was a wreck and that he left a suicide note behind.
It was just inconvenient for the pilot that the plane had been full of passengers at the time.