For a government agent or "luggage screener" to subject to harrassing scrutiny someone they know not to be a security threat is a counterproductive exercise. Not only does it generate ill will by the person who is harrassed, but it distracts from the task of finding real security threats. This is true regardless of the race or religion of the person being harrassed.
Selecting people for heightened scrutiny purely on the basis of race is a bad idea not only because it involves harrassing people for something they cannot change, but also because it may distract government personnel from noticing other people who aren't the targetted race but in fact pose more of a threat. On the other hand, selecting people purely on the basis that they're not members of a suspect race is no less evil and counterproductive.
Terrorists are profiling potential law enforcement officers in the same manner as they are being profiled themselves. To be innocent of profiling, you would have to be brain-dead. Perhaps this is the reason it is so appealing as an issue to some of our officials.