The thing is, every instance is its own server (virtual or physical). If it uses Cloudflare services somewhere, well...
If it uses some other stack, it'll be just fine. Neither of the two instances I'm on seem to use Cloudflare and hence the experience was uninterrupted for me.
While it might be a tough decision, I wholeheartedly welcome it.
Community-driven projects should be managed by the community, and I fully trust the Mastodon nonprofit to lead this part of the Fediverse into the future.
Good luck on this new stage, Eugen. And congratulations to all Mastodon users.