I'm going to throw my two cents in here now.
First off, a lot of things have changed with planes that have been mentioned earlier. You have reinforced cockpit doors ... which had these alone existed before 9/11 there probably would have been a drastic reduction in loss of life. The terrorists might have tried a hostage, a few people may have died, but 9/11 would have never happened.
Add in that some pilots carry arms and sky marshalls are patrolling the skies. Maybe not on every flight, but it'd be enough to make a terrorist think twice about the odds.
Lastly, you have pax that aren't going to stand for anything on a flight. Somone lights up, or if someone tries to storm the cockpit, people are going to bring them down.
Coming from the computer background, security is always an issue. However, this industry has learned that 100% security is a myth. It will NEVER happen. Even if it could be implemented, the system would be so encumbered that it wouldn't be able to serve the people and purpose it's intended to serve.
So you study the risks and mitigate the critical ones. You determine which risks need to be heavily fortified, and which ones need to be deterred, and which ones need minimal security, and go from there.
The question isn't will the bad guys get through the defenses. The question is when will they get through.
Terrorists are only going to strike when they have a high chance for success. Even if they did get on to a plane, they're not going to succeed. Pax won't let them.
TSA is trying to get 100% security, and they will fail miserably. They already are because our airports will never be 100% secure. Even tight government facilities aren't 100% secure.
TSA needs to seriously revisit security and determine what risks are the most credible. I think their vulnerability is in cargo screening and a bomb is going to be under the plane rather than in the cabin. Yet that doesn't get the attention it deserves.
Instead, they focus on the more minimal security risks, crank it up to the max, and cause serious issues for the people they're trying to protect: the pax.
I find it interesting that after the Unabomber threat passed, we went adjusted back and went on with life. I also find it interesting that it's easier to get into secure government buildings than an airport. Go figure.