This raises some interesting points about the established order of Apple in the tech landscape:
1. Around the same Apple was beginning a fight with FBI and law enforcement about protecting users' rights
2. That Apple didn't just pull the plug on Uber until it was fixed
That Cook had a meeting with Kalanick to warn him as opposed to acting unilaterally suggests that Apple doesn't have the power in the market that some believe (and that it projects).
Corporations aren't robots. They don't pull the plug on transportation infrastructure because of a TOS violation. There are plenty of disabled people who rely on Uber.
Taking Uber off the App Store would kill the company dead. Tim Cook had, has, and should continue to have that authority.
It wouldn't really though would it?
Everyone who had the app on their phone already would still have it and Uber would end up updating to comply pretty quickly.
When someone discovered that Uber suddenly needed your location “always” instead of just “while app is running”, Uber tried to say it was no big deal. Yet, combined with questionable attempts to profile users, it really does seem like they have a major interest in every drip of data they can scrape (namely, they probably sell it on the side).