"Using Tor or Truecrypt essentially paints a target on your back: you are paradoxically more likely to be under surveillance by agencies if you use them..."

"Paradoxically" you say. I don't think there's a paradox here. I think it's far too rare that people use these tools to protect themselves, and therefore the surveillance community sees it as a potential flag worth investigating.

Therefore, we should all use these tools, make them common place, and force them to learn to be efficient at their jobs tracking down actual risks.