All roads the hovercraft drive on need to have spatially-varying permanent magnetic fields. The hovercraft has a circuit with high induction sitting on board, but the circuit is usually broken. When you want to brake, close the circuit and power drained by the induced current will slow the hovercraft.
This could potentially be used to store the energy as well. The magnetic fields would have to be pretty strong, though. Perhaps installing superconductors underneath all the roads could do it, if that ever becomes feasible.
Another option would be to simply use the hovercraft's fan to brake. Usually, the engine drives the fan, which blows air out the back. You could make it so when you pull on the brakes, it works the opposite way. The air blows the fan, which sends energy back to the motor, or gets stored in a capacitor somewhere. This stops the hovercraft. You'd never be able to stop on a windy day, though, unless you stop actively by continuing the power the fan with the motor, but changing its direction.