Okay as a furloughed pilot who now (temporarily) works for the new TSA, formerly the FAA security division (not FSDO inspectors) I'll try to answer your reasonable questions to the best of my ability. First off I took this job to try and help improve security for my profession (that and it pays the bills while awaiting recall). Remember I also am an ALPA member, and am constrained on many issues by the importance to not release confidential material.
First off, if you have any problems at the security line, request to talk to the GSC (ground security coordinator). These are Air Carrier employees who must be at all checkpoints whenever they are open (if you don't see any air carrier rep contact any law enforcement officer and have them close the checkpoint until there is one present.)
Secondly, all screeners have been told that flight crew are not subject to the random screening that is too be done continuously at all checkpoints. However, if you have something in your bag that is suspect (i.e. a pair of scissors) then your bag will be searched. If you alarm the metal detector, you will be hand wanded. Many of us have shanks in our shoes, I go through the checkpoints 10-15 times a day and mine are always going off. I know they will, and I subject myself to the hand wanding. It doesn't hurt a bit and it only takes a few seconds. Don't blame the screeners for this, they are given a specific set of rules that they have to follow. Many of you'd be surprised how egotistical you sound saying that they are exacting revenge or trying to humiliate you.
If you do have to be hand wanded the screener is supposed to allow you to view your items on the x-ray belt while your being screened. If they won't do this have them call the GSC and explain it to him/her.
Oh, we know that you could crash the plane if you wanted to, and it probably wouldn't be very smart to announce that repeatedly at the checkpoint (a la US Airways), however, the screeners don't know much about airlines and if someone walked through with a Bin Laden Airlines ID badge and a pilots uniform on they'd think they were actually flying instead of a terrorist. Anyone can get a pilots uniform and many have been stolen along with ID's in the past year (I'd check more than one form of ID for any jumpseaters if I were you).
I'm all for a national ID for pilots. I used to commute to work and not being able to ride in the Delta/Southwest cockpit sure made it hard sometimes. Until that gets done (ALPA is working with the FAA but it will take time) be brave and go through screening like the rest of us. You probably only do it once or twice a day in reality (unless your in some terribly designed airport like MCI). You don't know how dumb you look when you make a scene at the checkpoint, trust me I've observed many pilots who think their gods gift and how dare you make me take my shoes off in front of the public.
Remember screeners are trained to do the same for everyone, they're not singling you out, in fact most screeners hate screening flight crews because they bitch and moan so much.
As far as the southwest pilot, if his own gate agent refused to let him fly, obviously the guy was more than the angel he made himself out to be.
Remember the screeners will all have to be federalized by Nov. 17th hopefully the testing, training, and hiring requirements will weed out the bad ones. Until then, you should see more standardization in the coming weeks (TSA just took over the supervision of screening from the carriers, but nothing can change overnight).
Keep your eyes open for terrorists, legally we can't profile, but we all do. There are many cells still out there and there is a lot of suspicious activity going on. Go to the FBI website and print out pictures. Carry them with you and look at people's faces. You never know what you might find, the life you save could be your own.
Flame me if you feel it makes you big, any legitimate questions I'll try and answer...I'm with the FAA (actually now it's the TSA) and I'm here to help you. (Ha, Ha).