There are a bunch of examples of this, to keep this simple; say there is an item in the cart that is tax exempted because of the user's location or for a hand full of other reasons. We allow you to individually set tax rates in a cart, as well as setting a general tax rate for the cart.
Each item in a cart can have a individual tax rate set to it, at time of checkout if a cart item does NOT have an individual tax rate applied to it. The tax rate that is set upon checkout on the cart is used.
Simply create a tax rate that has a rate of 0 and apply it to a product utilizing the Product Update