I think it's important to note this
1. El Al is a very small airline and Israel is a small country. It's easier to profile for a place where the air traffic is much smaller and there isn't a melting pot compared to the EU or north America.
2. El Al's security protocols are based on behavioral pattern recognition and not only racial or religious profiling. It is assumed they target arab muslims only because they are the purported enemies. In 1972, it was the Japanese group JRA who killed 24 people in Ben Gurion airport. Then there was the hijacker Arguello guy who was American I believe. How about that for racial profiling misses?
If we are to count extremists and concentrate on the muslims, then we are also screwed since all anyone has to do is change passport and religion. Chechen radicals are purported to be in collusion with Al Qaida. Can even the Russians tell the difference between a Chechen or a Georgian or even a Russian? They are both with caucasian backgrounds. Any system that picks race as a factor is flawed.
The Israelis claim they don't do only racial profile. However, with the overwhelming issues of Palestine and the Arab world, and being human, the BPR system is subject to human frailties, so naturally race does enter into enforcement. There are freaks everywhere in every religious and racial background.
To add to Eric's own experiences, I've been asked that very same question before at DFW, SFO, JFK, MIA and HOU (but not at LAX because my address is in LA). While I'm very aware that there's a certain act of self-consciousness when someone asks me that question, whereby I ask what sort of stupid question is that to ask me since my passport says it all? I do accept that if everyone else is asked that same question, then I'm the thin skin idiot who's hypersensitive. I've asked my caucasian friends who travel as much as I do if they've ever been asked that question. None have been asked that. Now why is that?
Behavioral profiling in theory is very sound when enforced by people who are smart enough to know how to do it. However, how many people with the intelligence to really profile a person without bias would work at TSA pay scales when they can get an equally mundane job in the private sector for much more money? Even then, can anyone say they are without bias? I'm sure some of it is out of ignorance or stupidity, but my point is that it is a flawed system. Eric's concerns about TSA's handling is valid and is being proven correct with the current system.
Now the terrorists aren't stupid either. Once they know the system, they'll find ways to pass it. That's what the PLFO did by using Japanese and Umar sewed explosives into his underwear. All this knee jerk reaction is hysteria. To stop people for getting up one hour before the flight lands? No potty privileges? The terrorist can't prepare 1.5 hours before the flight? Inflight entertainment switched off so the terrorist won't be distracted?
Well my new year's party had the same topic since a few of the people were flying back to the US. One of them had their flight cancelled ostensibly due to the crew trying to reprogram the inflight entertainment to switch off 1 hour before landing and it blew out the entire system, resulting in a cancelled flight. She saw it as a sign to stay and party 
Happy 2010...and unhappy travels with TSA apparently!