“Non-profit organizations” that sounds like the minority of developers

True but if you're a for-profit developer, you can probably afford 50 cents per customer. Facebook, for example, has a "free" app that earned $134 billion last year. I'm not defending Apple, I think the Core Technology Fee is anti-competitive and I hope the EU tells them it's illegal - but 50c is pocket change for nearly any for-profit app developer.

Small apps with less than a million users don't pay any fee either.

A million users is a big open source project and I think you'll find most of them already are non-profits. Or they're part of a larger non-profit that runs a bunch of projects such as the Apache Foundation, which provides funding and resources to almost 300 open source projects and could easily grow that number by a significant margin if there was much need for it. This potentially creates that need.

The main thing I have a problem with is the requirement to be an established "good standing" developer in order to deploy on the web. Apple's definition of "good standing" is clearly anti-competitive... I expect the EU told Apple they can deny distribution rights to developers who can't be trusted, but based on recent history (e.g. Epic) it's pretty clear that Apple and the EU don't agree on who can be trusted. They are surely going to have to change that rule.

I do think Apple can charge a fee to use their service. The EU is not banning fees and they never will. A government can't force a company to give things away for free. What I personally hope to see is the EU telling Apple that all fees must be optional. That way if Apple wants to make money, they need to offer something people are willing to pay for. If I was CEO of Apple, I would make the "Core Technology Fee" built into the price of an iPhone and make customers pay it.

That used to be Apple's business model by the way — and it worked. It wasn't as profitable as "give nearly everything away for free but force everyone to use this overpriced service", but Apple was still very profitable under the old model. And both customers and developers were happy with how it worked back then.