Given the potential destructive impact of a large airliner, it is better to be safe than sorry.
However, I think those of us who are not involved in national security can actually afford to discount this risk, particularly, when we make travel plans. The 9/11 terrorists whether knowingly or unknowingly took advantage of the fact that pilots too readily tend to assume that the hijackers are less likely kill people if they are appeased. I realize that there are many pilots on this forum, so I am less informed than them on this, but I would imagine that the protective impulse of many pilots, are to do what they can to save their passengers, crew, and the general public even at the risk of their own lives. I think given that we were unprepared for terrorists crashing our planes into buildings, their training was used against them.
In the sense that pilots were trained to appease hijackers, the terrorists were lucky on 9/11. We should have known that terrorists might try to crash planes into buildings, because in France terrorists tried to force an Air France plane to crash into the Eifel Tower.
I think we need to worry about the potential of a pilot crashing a plane. What is really scary is that apparently an backup copilot was able to crash the Egypt Air flight in 1999, and even when the pilot came back he wasn't able to prevent the tragedy. Another issue I'm concerned about is the issue of armed marshals. I think that it is hard to completely discount the possibility that in some countries, the marshalls could be infiltrated by terrorists or other dangers types of individuals. I actually think that it could be more likely that the marshalls get infiltrated than the pilots being terrorists. Remember, that the president of Egypt was assasinated by members of his own military at a military parade. We can link the group that killed Sadat indirectly to world trade center bombings.
I think the danger from a rogue pilot is lower than people think, but cannot be ignored. Fortunately, I think that the people who kill themselves to destroy planes are not a particularly talented or intelligent segment of their respective societies.
Just as we usually do not hear about the successes of American intelligent agencies, the big failures of terrorists never get reported either, which gives an erroneous impression of powerful terrorists, and inept Western intelligence.
Don't forget the attempt by Al Qaeda to blow up LAX
in 1999, which was a total failure, but got no press coverage whatsoever.