The protocols and software are all free and open source. You can’t stop a company from running a Lemmy or Mastodon instance any more than you could stop an individual from doing so.
The nice thing is that the system allows for free choice. Your favorite instance isn’t forced to federate with a hypothetical Meta instance, and and even if it does you can choose which communities to subscribe to or avoid. Who cares if Meta runs an instance, or a hundred instances? You can simply choose not to use them.