But pizza is a delivery food. Dominos doesn't even have seats. 90% of what it does is delivery. So the "overhead of running a delivery program" is just a business expense that should come out of their revenues.
Not sure if that happens in all cases, but I can see the case for charging a delivery fee. Baking it in to the cost of a pizza in general would unfairly charge people eating in or picking up. With delivery, you are paying for the pizza, and then an additional service.
I still think tips should be eliminated from the equation, though.