make addforce ignore player controller?

Hello Everyone, I am currently working on a 3d FPS game that enables the player to enter and pilot a underwater submarine pod. The pod uses the addRelativeForce on it's rigidbody since it slowly accelerates and drags as if underwater.

The problem is, my character's player controller is being seen as an outside force, even if I add the character (child) to the ship (parent) in the hierarchy.

If the ship does any sort of movement such as turning or ascending, the player is able to push against the ship and make it slow down or suddenly fly off into a random angle. The player has a rigidbody as well but with 0 mass,drag, and angular drag.

Does anyone know if there is a way to make the character controller unable to affect the addforce? I know I can use "position.transform.y" but then the ship doesn't react to outside colliders (such as rocks)..

Thank you for taking the time to read this, and I hope someone can point me in the right direction.

I have attached my script for the addforce in case it is needed.

 #pragma strict
 
 var theplayer: Transform;
 var theplayercamera: GameObject;
 var theplayermovement : FPSWalkerEnhanced;
 private var drawGUI = false;
 var thechair : GameObject;
 var theShip : GameObject;
 var respawnTransform : Transform;
 var respawnTransform2 : Transform;
 var seatOccupied : boolean = false;
 var chairCamera : GameObject;
 
 var driveCommands : startingshipdrivingscript;
 
 
 function Update () 
 {
     if (drawGUI == true && Input.GetKeyDown(KeyCode.E) && seatOccupied == false)
     {
         enterchair();
     }
     else if ((Input.GetKeyDown(KeyCode.E) || Input.GetButton("Jump"))&& seatOccupied ==true)
     {
         exitchair();
     }
     if (seatOccupied == true)
     {
         drawGUI = false;
         driving();
     }
 }
 
 function OnTriggerEnter (theCollider :Collider) 
 {
     if (theCollider.tag == "Player" && seatOccupied == false)
     {
         drawGUI = true;
     }
 }
 
 
  function OnTriggerExit (theCollider : Collider)
  {
      if (theCollider.tag == "Player")
     {
         drawGUI = false;
     }
  }
 function OnGUI ()
 {
     if (drawGUI == true)
     {
     GUI.Box (Rect (Screen.width*0.5, 400, 300, 26), "Press E to Pilot");
     }
 }
 
 function enterchair ()
 {
     seatOccupied =true;
     
     theplayer = GameObject.FindGameObjectWithTag("Player").transform;
     theplayer.GetComponent(MouseLook).enabled = false;
     theplayermovement = theplayer.GetComponent(FPSWalkerEnhanced);
     theplayermovement.walkSpeed = 0;
     theplayermovement.runSpeed = 0;
         theplayercamera = GameObject.Find("Main Camera");
     theplayercamera.SetActive(false);
     chairCamera.SetActive (true);
     
     
     theplayer.parent = thechair.transform;
         theplayer.transform.position = respawnTransform.position;
     theplayer.transform.rotation = respawnTransform.rotation;    
 }
 
 function exitchair ()
 {
     seatOccupied =false;
     
     theplayer = GameObject.FindGameObjectWithTag("Player").transform;
     theplayer.GetComponent(MouseLook).enabled = true;
         theplayermovement.walkSpeed = 6.0;
     theplayermovement.runSpeed = 11.0;
     theplayercamera.SetActive(true);
     chairCamera.SetActive (false);
     theplayer.parent = theShip.transform;
         theplayer.transform.position = respawnTransform2.position;
     theplayer.transform.rotation = respawnTransform2.rotation;    
 }
 
 function driving()
 {
 if (Input.GetKeyDown(KeyCode.W))
 {
  driveCommands.gear +=1;
 }
  if (Input.GetKeyDown(KeyCode.S))
 {
  driveCommands.gear -=1;
 }
 if (Input.GetKeyDown(KeyCode.D))
 {
  driveCommands.turngear +=1;
 }
  if (Input.GetKeyDown(KeyCode.A))
 {
  driveCommands.turngear -=1;
 }
 if (Input.GetKeyDown(KeyCode.R))
 {
  driveCommands.raiseup +=1;
 }
 if (Input.GetKeyDown(KeyCode.F))
 {
  driveCommands.raiseup -=1;
 }
 
 }