If you use certain camera modes, they can't. They can hover, but not fly. It's a great trick (plus it looks cool). If you haven't dealt with cameras before, just open up a new toy box, pick some big/visual centerpiece to throw in the center (one of the "set pieces", like Space Mountain or the Matterhorn, etc.) and just start playing with cameras and see what works. (It's a lot easier to figure it out in an empty box then to experiment in a box that is already developed, then once you figure out what you want to do just replicate it in the game you are making.)
Or you can always just limit it to super jump, because if you can super jump, you can't fly, but it depends on how much effort you want to put in on it.