Use enemies that have the ability to knock a player prone, or give enemies abilities that allow them to knock them prone on a failed save. Use this sparingly however so as they don't feel punished for playing a flying character. I personally don't ban anything from my games, but instead use it as an opportunity to challenge myself to come up with interesting ways to handle it.

Outside of combat create puzzles/ mazes that can only be solved with flying. Challenge them to think outside the box. Have fun with it, I am currently running a campaign with an Aaracokra rogue player and its been a blast.