Fan films are an interesting situation. The studio is not endorsing them so much and allowing them to occur, as they are a way of showing appreciation for the franchise.
JJ Abrams even had the man behind Star Trek Phase II/New Voyages, a fan production, have a guest cameo on the bridge of the movie.
It's a technically illegal, but partially tolerated/embraced facet of Star Trek fandom.
If there's no profit made, and it maintains franchise interest, then allowing fan films to be made is the sensible way to go.
It is unwise to antagonize the fanbase of a long running and profitable franchise.