Stress?
I am somewhat surprised that nobody has seemed to directly mention the word "stress" and the potential effects that this has on the ability of flight deck crew to perform their duties safely and efficiently.
Nobody is suggesting that flight crew should not be subject to some form of security screening but if they arrive at the aircraft feeling that they have been "unfairly treated" then, I would suggest, this must have an adverse effect on flight safety even for the most "laid back" individual. Pilots are in the front line of aviation safety and, in extremis, the feeling that they are not being correctly dealt with could lead to an aircraft accident.
I say this against a background of pilots having a longer and more arduous commute to and from work, often working right up to the legal limits and also at a time where other terms and conditions have been eroded. Not to mention the information in the "datasphere" feeding their psyches the idea that they may themselves have to deal directly with terrorism.