Anything that is purchased within an app, and ends up on your iOS device, must be purchased through the App Store. Apple charges the developer 30%, 15% for subscriptions after the first year. So of $9.99 charged through the iOS app, the developer gets $6.99 or $8.49. (Apple keeps $3.00 or $1.50, but has the cost of supplying whatever is supplied, putting it on their store, any charges, any losses because people have gift cards purchased with 20% rebate etc. )
Anything that is purchased from the developer's website, the developer gets the complete amount, except they have to pay for credit card charges, maintaining their website, and so on. Netflix obviously decided that this is more money.
The App Store rules say that the app _must not_ link the user to an external website. So anybody who downloads the Netflix app must figure out for themselves how to get to the Netflix website, or they won't become paying customers. That's the downside of not offering subscriptions through the app. Netflix has decided that these losses are acceptable, if they can keep more money from those subscribers that find their website.
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When they release their video service (or mixed media service), obviously they won’t charge themselves for In App Purchases, but all their competitors are still charged the 30/15% cut.
It's most common that companies charge themselves, because that is the only way they can find out whether something makes money or not. Let's say the top manager of "video services" reports proudly "we had $100 million revenue and made $10 million profits; I want a huge bonus", then Tim Cook will tell him "no you didn't, you forgot to subtract the 15% App Store fee, so you only had $85 million revenue and lost $5 million; you're fired."
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But what Netflix is doing now is freeloading. Using the resources of AppStore to seemlessly deliver their app and it’s updates to their customers without paying a dime. That ain’t cool.
Not at all. Apple offers any reputable company in the world a deal to put their apps on the App Store, as long as they conform to the App Store rules. We may assume that Netflix will continue following the rules. If they use the App Store in a way where Apple doesn't make money from the App Store, as long as they follow the App Store rules, then what they are doing is absolutely fine.
Companies that are selling products through the App Store that don't end up on your phone, like eBay, department stores, estate agents, and so on, always had free apps where Apple doesn't make a penny from the App Store.