How do I share Protocol Buffer .proto files between multiple repositories
This depends on your development process.
A git subtree / submodule seems like a sensible solution for most purposes. If you had more downstream projects, publishing a ready-made module would make sense, as then the protobuf generator wouldn't be needed for every project.
We, in the same situation, used 3 repos: server-side was written in c++, client-side in actionscript 3, and protobufs was in the third, and was used both of them. For a big team, and big project I think it was a good choice.