OS X cost $129 before Snow Leopard. Guess when Snow Leopard came out? In 2009, after the App Store. That's when prices started dropping, eventually to free.
It's obvious that the commission subsidizes the fee because the fee hasn't changed in 16 years. Apple's costs certainly haven't gone down. The commission scales so it obviates the need to raise the fee.
It's the cost of the iPhone which pays for iOS, iCloud, Maps and Siri and some other services. It also pays for the upgrades. You can see this as deferred revenue in Apple's accounting.
"For arrangements with multiple performance obligations, which represent promises within an arrangement that are distinct, the Company allocates revenue to all distinct performance obligations based on their relative stand-alone selling prices (“SSPs”). [...] The Company has identified up to three performance obligations regularly included in arrangements involving the sale of iPhone, Mac, iPad and certain other products. The first performance obligation, which represents the substantial portion of the allocated sales price, is the hardware and bundled software delivered at the time of sale. The second performance obligation is the right to receive certain product-related bundled services, which include iCloud®, Siri® and Maps. The third performance obligation is the right to receive, on a when-and-if-available basis, future unspecified software upgrades relating to the software bundled with each device. The Company allocates revenue and any related discounts to these performance obligations based on their relative SSPs."
-Apple's latest 10-K