Well, I didn't read this thread to the end, but I think I get the jist from the first 3 pages.
I am inclined to empathize 100% with the pilot quoted in the OP, and I often imagine myself doing the same thing if I were as glib and sharp tongued as he seems. In addition, I agree than TSA exists solely as a CYA agency for the powers that be, as someone posted earlier. However, there are several points that I much consider, and by which i must measure my initial reaction to the situation:
First, I consult the Fourth Amendment. As far as I can tell, like most amendments, it is fairly vague, and open to interpretation.
Whether or not body scanning constitutes unreasonable is up to the courts, I suppose, and cannot be determined by peoples' emotions and reactions.
Second, as someone mentioned earlier in this discussion, searches of this type are a consequence of a voluntary choice made by the individual, and are not imposed against their will.
So that being said, I do still see this whole ordeal as an erosion of personal liberties, but still, possibly, within the bounds we have set for our government.