The protocol of deployment is setup in the Publication Target on the CMS, this is done under Destinations in the General tab of the Publication Target.
The configuration of the Deployer is just specifying where to pick the transport packages up from, unless it is a HTTP/HTTPS Deployer, then the protocol is depending on the setup of the website (either HTTP or HTTPS).
So when you use a Local File System protocol or FTP, the Deployer configuration is basically the same, but the Publication target will have a different protocol in its destination.
The configuration of the Broker is completely separate and has nothing to do with the deployment of Transport Packages. The locations specified in the Broker configuration are where the files will eventually end up after deployment is done.