The insurance company values the car based on how it came from the factory, minus wear & tear. So they assume that you haven't "taken" anything from the car.
They are perfectly entitled to deduct for anything that was supplied with the car, but no longer there. (If the car came with alloy wheels, but you have steel wheels on the car, they can deduct for that too.)
If you want to argue (sorry, negotiate) about the value of the spare tire and jack ("these things go for $10 on ebay") you can do that.
BTW they also have to add the value of any permanent modifications (such as a permanently installed remote starter), but you'll have to prove the value.
-Bob C.
