...expect to be looked at somewhat suspiciously if I happen to park said boat in front of a nuclear sub facility...or should I be allowed to park it in the center of a shipping channel?
You are certainly allowed to use the airspace...however you are required to be licensed and you must meet certain requirements to operate inside said "air".
So while you consider it a "right"...it is pretty much handled as a priviledge (much like drivers licensing) and can have (and does) a certain measure of control over it dictated by the state.