You're confusing what they've publically said their business model is with how the store has actually evolved. They don't release figures that I know, so I'm not sure you can claim it is fact. It's specualtion on both our parts. As I said I wouldn't be surprised if they are making a small, but handsome profit from the store these days given it's success and the volumes they are selling.
Apple has sold about five thousand million songs on iTMS. The store would have to be run by a bunch of morons if Apple didn't make some significant cash from this. Every one cent of profit per song means fifty million dollars of profit for the company.
While the iTMS is beneficial for Apple as a whole even if it doesn't make profit, just like the Apple Stores would be beneficial for Apple as a whole even if they didn't make profit, and even though iTMS is only a tiny percentage of Apple's profit potential, you can be sure that there is a department at Apple that works very, very hard to make as much profit from iTMS as possible.
Just quoting Steve Jobs from memory (his words were probably different, and he said he learned it from someone else): "Profit is a small number that is the difference between two big numbers: Revenue and cost. If you have lots of revenue, you can make lots of profit". iTMS as a billion dollars revenue per quarter.