Photo Permits and Public Property

Photo Week #1
It's our annual Photo Week Celebration in which we answer questions regarding photography.
Dear Rich: I am an amateur photographer and have taken photographs of many public places within the city in which I live (e.g. parks, beaches, statues and other public works, buildings, streets). I compiled these photographs for an advertising campaign that I wanted to start of which the photographs would be used for commercial purposes. Now I find that a city issued permit is needed to commercially photograph, anywhere in the city. According to one city website, photographs cannot even be compiled, as part of a commercial portfolio without first getting a permit from the city, even if these photographs are not being sold. My questions is this: My registration for copyright at the copyright office is now in progress (although temporarily delayed at my request). Can I be penalized or fined by the city if my photographs are registered and made public (published) by the copyright office? Also, can I be sued for infringement if some of the photographs that I had taken and sent into the copyright office were of statues and other publicly displayed art works and buildings (which I now realize, may have been copyrighted by the artists). Start with the principle that a "permit law" created by a local government will have no effect on your ability to copyright your photos. Any permit law that attempts to limit your right to claim copyright would be preempted by federal law. In other words, even if the law says stuff about copyright, it would be invalid if challenged in court.
What's up with permit laws? Many cities and counties have permit laws for commercial photography and they're all pretty similar -- here's what Miami's law looks like. These laws require permits when shooting commercial photography in order to limit the impact of photo shoots on the public and to require  insurance in case someone is injured during the shoot. As this article points out,  the definition of commercial photography in these regulations is usually vague, so that a photographer who is not acting commercial -- working with models, props, crews, vehicles, or closing down traffic -- can usually manage without a permit.
Will the city chase you after the fact? It seems unlikely that a municipality will chase a photographer after the fact -- more likely if an incident occurred during the shoot. As for statues and public art, that's a different matter and we've discussed this issue previously (check out one recent example). That type of dispute involves the copyright owner and the photographer (not the municipality).
Today's public domain photo: from the U.S. Dept. of Agriculture photo website,  a 60-minute-old agar plate culture from an air sample taken in a caged layer room of birds infected with Salmonella enteritidis.