I mean if I start selling ebooks in the corner at Starbucks they may tolerate that but when Starbucks gets into the ebook business there should be a huge red flag going off telling you that the rules will eventually change: either they'll disallow my ebook sales or demand a cut.
Another huge red flag is a business model based on buying egoods from a wholesaler and reselling them in another vendors shop.
Another question: why couldn't they continue as a reader app and a web app store run by a separate company?
(the store licenses the DRM to the reader company)
If the answer is that the business doesn't work without the legion of customers the app store brings to the door that's another red flag.
I disagree with your analogy. iOS is not a store. The App Store is a store. I'd instead make this analogy: The owner of a bookstore is also the mayor of the town. He enacts a law (via declaration) requiring all bookstores to accept his bookstore's credit cards (of which he gets 30% of the sell price).
Luck for Apple they aren't dominant in ebooks. If they do the same thing to iTunes competitors (and it looks like they might), they could be in real trouble with regulators.
Speaking of bad analogies, iOS is not a town that Apple just happened to get elected mayor of. It's more like Disney World and Apple is Disney. Good luck starting your business inside Disney World without living by their rules.