Regardless how much money (revenue or profit) Apple may make from the App store or iTMS, it is a complete misunderstanding of Apple's business model when you say that Apple could sell an iPad for cost and still make money.
Apple's business model is about profiting off their hardware. Apple is a hardware company, they make their money off hardware sales. The way they make their hardware interesting and valuable to consumers different to other hardware manufacturers such as Dell or Gateway or HP or Asus is to create an infrastructure that runs on and makes their hardware "sing". Whereas companies like Dell and the likes, manufacture and sell hardware, they require other companies to produce and sell stuff that makes their hardware even function. Apple is not like those hardware companies, Apple produces and controls the infrastructure that enables their hardware to be the greatness that it is.
They didn't create the iTMS or the App Store to make money, they created these entities to create and add value to the hardware they produce. The fact these entities *may* make Apple some money is irrelevant - Apple is all about hardware, and these entities make their hardware more valuable and that's one reason they can sell their hardware for more than other manufacturers of hardware.