Whether $99/yr is enough to cover costs or not is beside the point. You also don't seem to acknowledge that having these apps available on the App Store helps Apple sell more iPhones and other devices and services which more than offsets costs.
That's why Apple doesn't charge Amazon, McDonald's, Walmart, Bank of America and similar apps where Apple gets $0.00 in commission anything more than the annual developer fee. It's also why Apple's willing to offer some companies sweetheart deals...
It’s leverage. The reason is leverage.
www.theverge.com
Apple and Amazon very, very quietly unveiled a monumental app deal this week, without fanfare or, sadly, much in the way of transparency. Out of nowhere, buttons to buy or rent movies appeared in the Amazon Prime Video app. It’s difficult to express how strange this is: for over a decade, Apple has stuck to the rule that all digital goods sold in iOS apps must use Apple’s payment methods, including Apple’s 30 percent cut.
Suddenly, that rule appears to apply to all developers except those who have the leverage to cut a special deal with Apple.
It's a strategy similar to how supermarkets operate. They use loss leaders (e.g. milk and eggs) to get customers in the door, hoping that they'll buy other items, especially items with higher margins.