I agree that such large apps are treated somewhat differently than smaller ones—anyone smaller than Uber would have been banned outright. That’s due to demand from Apple’s customers, though, and not Uber directly paying Apple.
But Uber still had to rush and submit a new version of its app. They didn’t seem to believe Apple was making hollow threats, nor do Facebook and Google and all the other big players adhering to Apple’s policies.
Even if Apple wanted to allow larger apps breaking the rules, they couldn’t. It would be very obvious if some apps were allowed to send ads and others weren’t, and it would lead to all kinds of problems in the court of public opinion and possibly a real one.