Over flight fees for Puerto Rico are determined by the FAA. Those fees are standardized and are as follows:

**There are only two different rates for flying through US-controlled airspace. Flying over US land, the "en-route" rate is $61.75 per 100 nautical miles. However, when flying over ocean monitored by the FAA, that rate drops down to $26.51 per 100 nautical miles.

And, Puerto Rico does not "own" SXM airspace.