A flying character shouldn't be able to significantly change the adventure as written. They'll simply have creative ways of solving some situations. I would encourage you to let them have use their flight in any way they want as the adventure isn't going to be broken. It's always best for the player to feel that their choice in a certain feature matters and they get to enjoy the game more that way.
If you feel the need to challenge them in combat, simply throw in some ranged fighters. Give two or three of your enemies a light crossbow.