The system is working AS PLANNED.
The Gore Commission, formed after the flight 800 explosion, proposed several regulations that were watered down due to protests from the usual suspects. One that was finally implemented was something called CAPPS (Computer Assisted Passenger Pre-screening System). It was a profiling system that had the unfortunate property of being accurate. This lead to complaints and protests from Arab groups and the FAA started backing away from those procedures designed to investigate passengers flagged by CAPPS. They finally achieved their goal, which was ZERO complaints per year from all Arab passengers.
On 9/11, CAPPS flagged the majority of the hijackers. However, nothing was done to investigate any of them, because there was no method of doing so without alerting them that they had been flagged, and that might lead to a complaint. They couldnt even ask them a simple question, like Why are all of you carrying box cutters?
After 9/11, the government was caught in a quandary. How do they appear to be doing something about airline security, when all of the hijackers fit a specific profile, yet they dont want to be accused of profiling? Why, you design a system that is so incompetent and overbearing that all kinds of people are inconvenienced and burdened. Then if a special interest group was to complain, you could point at those other people and say, Were not profiling, look at what that grandma in a wheelchair went through!
In fact, this newspaper story about a white guy from Texas being shafted (thats right, Im profiling in assuming that a hunter and fisherman from Texas that travels to Alaska regularly to hunt, is white, and everyone that reads the story will assume the same thing) is just what the FAA likes to see. Its free publicity and helps keep the Arab special interest groups off their back.