I think we are safer in the sense that both crew and pax are now aware of the threat from suicidal terrorists. For example, the shoe bomber was only stopped thanks to this new level of awareness. Prior to Sep 11, he would probably have succeeded, and if the plane had gone down, it's unlikely that anyone would have known why.
Future hijackers and suicide attackers will probably need to be present in larger numbers or have more powerful weapons in order to succeed, which might be harder to accomplish with the new level of security, however cack-handed it might be.