What I wonder now is if these federated communities are immune to this. For example, can I host an instance that publishes ads to subscribers feeds once I reach a critical mass of users?

Yes, this is a thing an instance admin can do, though some Fediverse platforms make it harder than others. A very large chunk of the Fediverse is then going to defederate with that instance because they hate that shit. So in this regard, there is at least some counterplay in that users still have a decent amount of control over their own destiny. If one big instance goes to shit, the other instances can still maintain their standards and aren’t forced to abandon the platform if they don’t like the trajectory of one particular instance. Users of the big instance who don’t like said instance’s approach also have the option to migrate to other instances, so they’re not held hostage.