Character Controller problems with a space ship

I am making a game where a character can walk into a spaceship and fly it. At first i put a rigid body on the ship but every animation, opening the back door and the cockpit door, throws the ship around. I changed the rigid body to a character controller because i thought that I could do what I wanted with the rigid body through code in the character controller, but the only collider on the ship now that actually collides is he character controller. (I added a couple box colliders here and there on the ship so i could save memory by not using a full on mesh collider, on the rigid body the ship would sit on the ground with the landing gear, but with the character controller it falls through the ground until it hits the character controller then stops) how do i fix that the colliders still collide?

hope that makes sense, and thanks for all the help.