We’ve done exactly that, flying SW from Orlando to San Juan and then catching an InterCaribbean flight with a short layover. No issue if you carry on only. When you get off the SW flight walk over to the IC gate and wait for the agent to arrive. Don’t panick if no one is there... the earliest they get to the gate is 1 hr before the flight departs, and often later. Once they arrive at the gate the ticket counter closes, which is why you will not make it if you check bags and therefore have to recheck them in San Juan. We saw this happen to someone on our last trip (end of January) and part of their group had to catch a later IC flight.

Save the money and go for it. Worse thing that happens is you have to catch a later flight, but it has never happen to us.