Their stance makes perfect sense. The App Store is not a commons, it is the private property of Apple, in which they curate the works of others at their convenience.
But unlike a book store or a music store, they can closely associate what they stock with the brand becaues the "App" medium is so new.
It's pretty similar to a local coffee shop maintaining a few book cases for customers to borrow or buy, but being pretty strict about what books can be put in their selection.
Ultimately, I suspect they are more controlling about apps than about books or music because apps are (or were) a new medium that, for both financial and marketing reasons, they wanted to think about differently. Apple probably feared (and/or hoped) that Apps would have a more intimate connection to their brand than e.g., the tracks in iTunes.
(edit: 1. Not saying I agree; 2. this post is a descriptive conjecture about why/how Apple treats apps differently, not an advocacy that they continue to do so. Jeesh.)