Each nation "owns" its own airspace under the
Chicago Convention. I don't see any provision for charging or not charging for the use of airspace, but they can certainly charge for the use of airports and air navigation facilities.
In the US, any local law governing the right of passage of aircraft is preempted by federal statute. This eliminates the possibility of every little burg charging aircraft for passing overhead.
The "air" issue in this article is different, since it involves a permanent structure overhanging someone else's land. I wouldn't want that either. A little stupid that the city didn't bring that up earlier.