I understand the concerns around a central gatekeeper but I'm confused as to why this specifically is viewed negatively. Don't website owners have to choose to enable cloudflare and to opt-in to this gate that the site owners control?

If this was cloudflare going into some centralized routing of the internet and saying everything must do X then that would be a lot more alarming but at the end of the day the internet is decentralized and site owners are the ones who are using this capability.

Additionally I don't think that I as an individual website owner would actually want / be capable of knowing which agents are good and bad and cloudflare doing this would be helpful to me as a site owner as long as they act in good faith. And the moment they stop acting in good faith I would be able to disable them. This is definitely a problem right now as unrestricted access to the bots means bad bots are taking up many cycles raising costs and taking away resources from real users