>I think these are in place. Last time I saw a flight map for a city, there were huge no fly circles around it. I'm not a pilot but I think that's been around for a while.
Except in very specific cases (most of them TFRs, with a few permanent restrictions, specifically IIRC, Washington D.C.) there are no restrictions about flying over cities. According to FAR 91.119, you must be 1000 feet above the highest obstacle within a horizontal radius of 2000 feet (obviously, except when conducting landing or take-off operations at a designated airport).
In addition, you need to be in contact within any the controlling agency while within controlled airspace.
For example, I can fly over Seattle, at or above about 2100 feet AGL, as long as I am below the overlying class B airspace, without talking to anyone or even filing a flight plan.