Yes, this kind of stuff does infringe in our rights. I feel like the pilot did the right thing here.
But let's take another step in a different direction:
Why are we even bothering? These new scanners are an absolute waste of money and resources. If a terrorist truly wanted a way to sneak in bombs and cause harm to civilians, there a number of ways to smuggle such things in and deploy them in a very deadly manner that would have little to do with airplanes. This new security policy is totally useless along with being constitutionally threatening; in the end, an inconvenience, no matter how small one may feel it is.
It is remarkably easy to just walk through these and not give a damn; in turn, it's also remarkably easy to be totally ignorant of how much of a detriment these new methods are, both economically and legally. They could be using these resources to improve the quality of your flights... why would someone be content with useless scanners when they could be having better quality flights instead?
WhySoBluePandaBear: What is with your obsession with tiny penises and licking windows, huh?