While choosing a class does not limit you in your capabilities, e.g. a Gunner can repair and drive the ship, each class carries more of their class specific tools and equipment. Captains (first slot in ship load, and normally also a Pilot) can kick other players off the helm.
Gunners and Engineers are recommended for players who have not played the game before. Their roles are fairly straight forward and easy to pick up. Engineers are responsible for repairing ship components and keeping the ship alive. They can use a variety of repair tools to both add HP to components, as well as to rebuild them if they die. Gunners can bring the most special ammo aboard and load into ship munitions. Ammo can greatly change the behavior of weapons so using the right ammo of the right guns, and at the right time is a skill unto itself. The game features realistic ballistics physics for many of the weapons so be sure to lead your shots. You are on a moving airship, after all.
Pilots are for recommended for experienced players who those who show a penchant for leadership and strategy. Pilots and Captains are usually synonymous and will choose the ship and select its guns for a particular match. The ship and its guns is the first strategic decision that a Captain makes. It might be a fast ship with flamethrowers, or a heavy ship with broadside cannons. Each has a different role to play in combat. When in a match, the Pilot is responsible for maneuvering the ship in and out of combat. It also means the Pilot has the most situational awareness in combat and should instruct crew on what to do whether it be getting on port side guns of all hands repairing the Hull.