Confiscating everyday items classed as 'potential weapons' from a genuine pilot is of course utterly absurd. But I think many here miss the point. The screeners do not know you are a bona-fide pilot (or CC) on your way to operate a flight. Anybody can buy a pilot's uniform (mine still fits), and identity cards can be faked/stolen as others have said. And the screener can't tell if you're driving or deadheading.
It seems to me there are a couple of things which could be done.
1. Set up a separate line for crew, and put it behind screens so the pax can't see the indignities being inflicted. Obviously only appropriate at large airports with multiple screening stations.
2. Better yet, remove crews from the concourse screening entirely. Get screened in dispatch or wherever and then be driven airside to the flight. If you spend the rest of the day in secure areas you don't need to be screened for subsequent rotations. If you do need to switch concourses then again do it airside.
A few minor logistic considerations perhaps, but better than the status quo surely ?