Hi Mike,
Yes, those are actual comments I've heard from people I've talked to about this. Even those who do care about civil liberties generally take the view that "there are more important things to worry about," or "well, sometimes we have to sacrifice a little essential liberty in exchange for short-term security." I guess we as railfans are more acutely aware of our rights to do things that to some may seem suspicious, nerdy and/or esoteric (taking pictures of trains, studying track maps, playing contingency games about taking lines out of service, not to mention a healthy amount of gummint-bashing) than the general public. It's a sad commentary on our society.
Just be careful when you get off the train to not be too "suspicious," or you might convince your surveiller that you're attempting to evade law enforcement (which in fact you are, I guess), which would invite an even bigger response. Be prepared to spend the better part of that day in an interrogation room - you'll be released without charge and with all your possessions if you give the right answers, but you can forget about whatever you were doing that day...