Bonnet Creek, like Reedy Creek, is an actual creek that runs through Disney, in fact that is what you see outside of the restaurant window. Anyway, since it's an actual body of water, the name can't be copywrited, so the new resort "borrowed" the name also. To avoid confusion, Disney simply gave up and dropped the name from the golf resort. At least that is the story I got.
For those of you who have never visited this location, Mickey's golf cart is located here, and is located near the score board, makes for great photo ops!