The one issue about a security check that is designed to deter is that it has to be very visible, especially on those attack routes that are easiest. The fact that a potential terrorist can see aircrew going through the same security checks as everyone else is in itself a deterrent to masquerading as flight crew.
Can anyone actually produce some evidence of a situation where a terrorist dressed as a pilot hijacked an aircraft? Of course we all know about Frank W. Abagnale and his efforts to travel around the world masquerading as a pilot, but this was definately a one-off ocurrence and with the measures to keep unauthorised people off the flight deck these days, it seems unlikely that someone could repeat his efforts.
We all seem to forget that the 911 terrorists weren't pretending to be pilots. They didn't have uniforms on. They were simply passengers with a limited understanding of operating an airliner. Now we have locked flight deck doors and a very good reason is needed to open those doors in flight.
Given these facts, what is the real reason for security screening pilots with passengers?