This post is tangential to the issue at hand, but has real and true anecdotes designed to be mildly entertaining. Read at your own risk.
We had airport security before 9/11. What is unknown is if our current organizational system is a) more effective and b) whether or not there could be simpler/less intrusive ways to gain the same level of effectiveness.
I have a personal story. I was on the Carlos the Jackal list for a while. Several very inconvenient situations arose from this. Once after a conference in Rome, where I had done a poster presentation (in science you either stand in front of an audience, show some slides (powerpoint usually), and talk for 20 minutes with a 5-10 minute period where people try and rip you apart or you stand in front of a poster that summarizes some aspect of your work for 3 hours while people wander by and ask you questions about it). I had the poster rolled up and put in a big poster tube and in order to separate dirty underwear from clean underwear I had shoved about 6 pairs of dirty underwear into the tube. Another bit of necessary background is that I had what is commonly known as the stomach flu and needed to visit the bathroom about every 27 minutes or soil myself. Anyway, I got pulled aside, was surrounded by these dudes that were accompanied by German Shepherds and had uzis slung over their shoulders whilst they pulled my underwear out of the tube one by one. The dude doing this examination would even take a pair of recently worn whitey tighteys and hold them up to the airport's fluorescent light for closer examination. They missed the giant poster in the tube and asked me questions about the tube until I pulled the poster out. Personally, after underwear pair #1, my investigation would have been over. However, I do think I looked suspicious since I kept glancing nervously over at a bathroom that was about 50 yards away which I sprinted towards after I had been cleared.
On one family vacation to WDW (we usually drive, but not this trip), my family was able to check their luggage in at the resort for our upcoming flight and get boarding passes (Southwest flight, Boardwalk if I remember correctly, circa 2008). I was not able to do either and had to go to the airport and have my luggage examined etc. This meant that I had to go to the airport early and missed some family fun time.
My typical check in procedure at the airport would go like this. Gate agent types in all my info. Eyes momentarily widen and then my driver's license is whisked to some back room. They are gone for a while. Then the gate agent would come out with a more serious person wearing a suit and I would be asked the normal security questions in a more stern tone. My bag would then be opened and every item examined (this didn't happen every time, but it did happen about 70% of the time). I would always have to run my luggage through the super luggage scanner. I could oftentimes leave it while this was done. I had to allow for 30 extra minutes for this and the worst thing on my rap sheet is speeding tickets. For a while they would put a little circular sticker on my carry on, but they quit this.
I flew just enough that this inconvenience was intrusive, but not so intrusive that I worked on the problem right away. However, after that Disney trip, I started to investigate the process of getting my name off the list and sent several letters to TSA/DHS. At some point, I got a letter from DHS saying my name had been removed from the list. I haven't had a problem since. The letter also said that I could never know why my name was on it and that I could be put back on the list at any time.
It has been 5 or 6 years since I went through the name removal process and have tried to recall things the best I could. I see now their is webpage for traveler's who had issues like I had,
http://www.dhs.gov/dhs-trip (trip stands for traveler redress inquiry program), but I don't think it was quite this well organized back when I did it because I remember web searches being fruitless. I kind of remember asking TSA people at the airport and making a few phone calls before discovering who I had to write letters too.