Let me add a bit to this if I may.....
Remember the Top Gun school in the movie? That was filmed at the real Top Gun school that was the Navy Air Base at Miramar. It has now been turned over to the Marines - and is the Marine Air Station. They fly jets as well as helicoptors.
Miramar is located toward the northern end of San Diego and is really surrounded by the city - residential/business development. The Air Station was there long before development of the city extended out to it.
Miramar is a vitally important link. The Western Pacific Fleet which is based here - all those air craft carriers - those planes are based at Miramar. They train there, are repaired there, etc. When the carriers come into port, the planes land at Miramar.
Since the city now extends around the base, the Navy pilots have to fly in all sorts of circuitous routes as they practice touch-and-go tactics so as to minimize the amount of noise they create. Residents complain - however, the base was there first. Everyone who has bought a house in that area knew the base was there and that there could be a noise problem.
I recently read that another concern is the flight path of the miliatary jets disturbs some nesting birds and so this is another item the pilots have to take into consideration.
And then there is the issue of the vernal pools. You can read a description of them here:Vernal Pools
As I understand it some of these vernal pools are on Camp Pendleton and when the marines are practicing in their tanks and jeeps, they have to avoid these for quite a distance around.