Putting aside the fact that the App Store is profitable.. why does it have to be?

Why does it have to be profitable? Because if it isn't it goes into debt and eventually shuts down.

Companies are not required to nickel and dime consumers for every offering, and often time goodwill generates more revenue as a whole than squeezing every penny.

You are absolutely right. This is one of the reasons there are so many mergers; it allows companies to do this with little to no alternative. See cable companies, Ticketmaster, Facebook, Microsoft, etc. You want to squeeze your customer base without having to worry about them going to your competitor? Buy your competitor!