Clarify when “hub.protocol” is applied

From https://github.com/github/hub/issues/665, there might be some confusion on when "hub.protocol" is applied.
Trying to clarify a bit more here. This PR depends on https://github.com/github/hub/pull/666.

/cc @mislav
This should be clearer:

> "hub.protocol" only applies when the "OWNER/REPO" shorthand is used instead of a full git URL.