Solved the problem my self with 1 easy trick.

Just added another empty gameobject to the ship and let this control the players position and rotation. In update() of the real playerobject script I just set its position to the empty gameobject which is parented to the ship.

So easy, but it was hard to find out this solution.

why does your ship need to move when the player is inside? if the player isn't visible you could just destroy him and assume control of the ship then instantiate him when your done controlling the ship. Or if you control your player while inside the ship but still want your ship to "move around" you could try moving the rest of the level around the static ship OR you could put animating textures in the windows to simulate outside movement. Another fix if you definatly have to go down the route you described just code something like rigidbody.isKinematic = true; which activates when your player is parented to the ship and of course false when you unparent him (assuming you unparent him at all)

Here is some code I used in the script attached to the player:

var playerParent : GameObject;

function Awake () {
   transform.parent=playerParent.transform;
}

function Update () {

if (lastPosition.magnitude==0)
{
   lastPosition = transform.localPosition;
}
transform.position = transform.root.position+lastPosition;
}

Works fine, as well as the parent is not rotating.

To rotate lastPosition (the position of the player inside the ship) correct to the ship, I need the correct rotationangles of the ship. Then I can rotate lastPosition (as playerDistance in this example) with this (:

var X : float;
var Y : float;
var Z : float;

    Y += (playerDistance.y*Mathf.Cos(shipRotationAngles.x) - playerDistance.z*Mathf.Sin(shipRotationAngles.x));
    Z += (playerDistance.y*Mathf.Sin(shipRotationAngles.x) + playerDistance.z*Mathf.Cos(shipRotationAngles.x));
    X += (playerDistance.x*Mathf.Cos(shipRotationAngles.y) + playerDistance.z*Mathf.Sin(shipRotationAngles.y));
    Z += (- playerDistance.x*Mathf.Sin(shipRotationAngles.y) + playerDistance.z*Mathf.Cos(shipRotationAngles.y));
    X += (playerDistance.x*Mathf.Cos(shipRotationAngles.z) - playerDistance.y*Mathf.Sin(shipRotationAngles.z));
    Y += (playerDistance.x*Mathf.Sin(shipRotationAngles.z) + playerDistance.y*Mathf.Cos(shipRotationAngles.z));

var newVector = Vector3(X,Y,Z);

...and then I could do:

transform.position = transform.root.position+newVector;

So the question is, how to get the right angles? transform.root.rotation is a quaternion which gives wrong angles if I want them to use with this script (real 360 needed).

Any ideas?