Prosecutors could just be exercising their prosecutorial discretion, but if they thought that Apple was acting in violation of anti-trust law, I believe they would prosecute. They've done it before (the eBook case).
This is purely an opinion, as this case hasn't been tested in court, so there is no case law to cite for you, but I believe the facts in the Mircrosoft case can be distinguished from the facts in Apple's case because Apple doesn't have a monopoly on the smartphone market. Over the past few years, Apple has had between 15 and 20 percent of the smart phone market by unit:
Contrast that with Microsoft's 90%+ market share in the 1990s.
Since Apple does not have a monopoly, it is not taking advantage of a monopoly when it forces particular default app choices on you.
In U.S. v. Apple (the eBook case), the anti-trust behaviour didn't involve only Apple, but also Hachette, Harper Collins, Macmillan, Penguin, and Simon and Schuster (who, taken together, had 48% of the eBook market as of Q1 2010). Thus, this is distinguished by the type of behaviour that happened and the magnitude of the market controlled by the defendants. Price fixing amongst ostensibly competing publishers that will sell on Apple's platform is drastically different behaviour than what you are asking about in your question.
I don't believe that Apple actually price-fixes any of the apps sold in the store. App publishers are free to choose a price from a large variety of tiers.