I'm sure Apple is very pleased with the profit margins they get on in-app payments, but I'm equally certain that Apple's desire to keep people using their payment system is just as much about maintaining a great user experience for users.
Obviously the flip side is that some companies - Netflix! - then decide just not to offer payment in-app at all. That's also bad! But I don't know how to compromise on allowing apps to direct users to payment systems outside the app store without opening the floodgates to a million different payment experiences, which I (again, selfishly) would love to avoid.