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
The ronn file only uses the [examples](https://github.com/github/hub/blob/master/man/hub.1.ronn#L202) from the README. I could change it to use the configuration section as well in another PR though.