PyPI has paid organization accounts now which are beginning to form a meaningful revenue stream: https://docs.pypi.org/organization-accounts/pricing-and-paym...
Plus a small fee wouldn't deter malware authors, who would likely have easy access to stolen credit cards - which would expose PyPI to the chargebacks and fraudulent transactions world as well!
If pypi charges money, python libraries will suddenly have a lot of "you can 'uv add git+https://github.com/project/library'" instead of 'uv add library'.
I also don't think it would stop this attack, where a token was stolen.
If someone's generating pypi package releases from CI, they're going to register a credit card on their account, make it so CI can automatically charge it, and when the CI token is stolen it can push an update on the real package owner's dime, not the attackers, so it's not a deterrent.
Also, the iOS app store is an okay counter example. It charges $100/year for a developer account, but still has its share of malware (certainly more than the totally free debian software repository).
Though I do like your Apple counterexample.