Let's say (for now) that this nation's sorry history of racial oppression makes it untenable for us to profile on the basis of ethnicity. That doesn't prevent us from seeing that the terrorists were all men. Given the treatment of women in conservative Muslim society, it's not terribly likely that bin Laden is going to be training and arming women any time soon. Training women to rise up against oppressive governments is the last thing the conservative Muslims want to do.
In fact, even our homegrown terrorists are men. While profiling by race might miss the next Timothy McVeigh, profiling by gender would not.
It stands to reason that if we scrutinized women a little less and men a little more we'd be putting our security resources to better use.
Would it be fair? As a man, I'd be inconvenienced more than a woman for a factor over which I have no control (my gender). It wouldn't be fair, but it would be smart.
Since men have traditionally had it pretty well in the US (and everywhere else in the world—go figure), we're not sensitive to being scrutinized for our gender the way ethnic minorities are sensitive to being scrutinized for their ancestry. My guess is that men would deal with the unfairness pretty well.
On a related note, a 2001 incident in Seattle shows that men are more sensitive about ethnic identity than gender identity. When a white police officer shot and killed Aaron Roberts, the black community was outraged that another black had been killed by the police. No one cared that another man had been killed by the police. While records show that blacks are killed by police disproportionately in Seattle, no one bothered to point out that men are also killed disproportionately. But the men of the community didn't care that yet another fellow man had been gunned down, even though the statistics show that men are apparently being "singled out" or "profiled" by police.
Now, if we think gender profiling it a good idea even though it's unfair, does that mean that ethnic profiling could also be a good idea even though it's unfair?
New York police have begun searching bags of riders on the transit system. Bags to be searched are being chosen at random even though the ethnic and gender make-up of the people we're afraid of is anything but random.