Ignore Collision with Character Collider

I'm using the following code to ignore a collision with my player, but it only affects the player's box collider and not the character collider(It has both). Since the script uses it to move the player, it can't be removed. How do I ignore the collision with the player's character controller.

function Start () 
{ 
    player = GameObject.FindGameObjectWithTag("Player").transform; 
    Physics.IgnoreCollision(player.collider, collider);

} 

Edit: It has to be done via script since, not Ignore Collision Layers in the project settings, since the project settings don't transfer over to Unity on other computers.

Every GameObject should have only one collider attached, especially a CharacterController. If you need more than one you would add another GameObject (as child). Anyways, if you attached another collider you can't use the .collider property since it only returns the first collider. You just have to use GetComponents like you have to for other components.

function Start ()
{ 
    var cols : Collider[] = GameObject.FindGameObjectWithTag("Player").GetComponents.<Collider>();
    for (var C : Collider in cols)
    {
        Physics.IgnoreCollision(C, collider);
    }
}

you can disable collisions in the physics project settings. you need to set up layers to define which objects can collide with which, then make sure your game objects are assigned to the correct layers.