Apple makes money through iPhone (and iPad) sales. That is what pays their costs for maintaining the App Store for free apps. Apple could enforce a minimum price, but it has decided that in balance it profits more from the presence of all the free apps that help generating iPhone sales than the App Store running costs the free apps cause. Plus there is also the aspect that a good deal of free apps come from developers that also have paid apps (upfront, in-app, or subscription), allowing the free apps helps those developers which in return does help Apple via their paid apps (both directly via the 30% fee and indirectly via iPhone sales).
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Do you know when exactly this happened? It must have happened before 23 Aug 2018, as
this article from that date mentions that they had stopped accepting in-app subscription.