Providing even a free native app via the App Store to access a service with a subscription model becomes a very risky proposition given Apple's rules, though.
[0]: http://app.ft.com/
This is where things get pretty shady with Apple's terms for native apps and the App Store. Take a look at Spotify's experience for a different version of the story.
[1] https://www.statista.com/statistics/296226/annual-apple-app-...
> In the last reported year, customers spent an estimated 54.2 billion U.S. dollars on on in-app purchases, subscriptions, and premium apps in the Apple App store.
So, roughly 30% cut goes to Apple - which is around 16 billion; and developers got the rest, around 38 billion.
With PWAs, 100% goes to developers. As you pointed out, that's a threat and motivation for Apple to continue racheting up their closed ecosystem, and keep PWAs crippled on Apple devices.
As lliamander said, if they don't care, why not make it free? I don't for a moment believe the argument about creating a barrier for negative actors. They could still screen apps before allowing them into the App Store, and if that mechanism is working reliably then the charge is unnecessary as a deterrent, while if it is not then the financial deterrent isn't going to be enough to stop a lot of people willing to make these kinds of apps anyway.