Chris - I do know of a couple of incidents, one involving a professional photograher that I know quite well (taking pictures of the US Embassy with a photography class from the local community college) and another involving an amateur that I know taking a picture of an OCTranspo bus (local city owned transit service) who were hassled by the police and by transit security.
In both cases, the photographers were well within their legal rights. In both cases law enforcement was not as enlightened as the ones you have run into. It's a bit like Colin's example above (#4); being right is not the only consideration. I enjoy taking pictures; I do not enjoy irritating and upsetting people.
That being said, a copy of the PDF will be going into my camera bag.