The blog at Photoblogs.org has a post about a ban on photography inside the San Francisco MUNI system (buses), and a similar ban inside subways.
I have had a similar experience a short while ago when I was taking pictures of a sunrise from the sidewalk of a freeway bridge in the Bay area. Suddenly two police cars came in from both sides of the street and I was asked to back off from the sidewalk and was questioned for about 40 minutes about what I was doing. I showed them the photographs I took of the sun and there were no traffic or buildings in the pictures. Feeling a little silly, the Police officers told me that even though it is not illegal to take pictures in Public I should avoid taking pictures on bridges and then they went on and on about how some people jump from the freeway bridge and throw cans on the incoming traffic. But the lesson I learnt from the whole episode was that photography is not worth getting in trouble with the Law :)
Here's a directory of Camera policies inside privately owned public places.