Not specific to protobufs but a lot of people/projects especially if doing MVC, push the models in the API layer all the way down the stack and they become the domain, instead of having a loose coupling between the domain and serialization format. In the old days we used to have DTO's for separation but they went out of fashion.

Agreed, it's interesting to see so many people complaining when they are just misunderstanding / misusing protobufs entirely. Sure the implementation could be better but it's not a huge problem.

Like the author said, their usage in practice often creeps outside that.