Not a super-expert but I've used Vapor on some personal projects. Do you have a link to the mention for "protocol server"? I'm not familiar with the concept but might be able to help.
In this instance they're talking about implementing network protocols, such as HTTP, where one end is the client and the other end of the connection is the server.
It's confusing because the Swift language also has the concept of "protocols" which are basically the equivalent of Java and C#'s interfaces if you're familiar with those languages.