To "fly the ship" means to operate or pilot a spacecraft or aircraft. It refers to the actions and skills required to control the vehicle and navigate it through the air or space. Full definition
The highlight of flying the ship around is the music, which is the music directly out of the ride. (vinylmationkingdom.com)
The controls for flying the ships are just a mess. (elder-geek.com)
From the start, you have plenty of these that allow players to jump into a specific scenario in the process, such as just flying a ship rather than worrying about building it. (attackofthefanboy.com)