The default transport allows optional security via TLS/SSL. Since some clients (for example in embedded systems) cant use certificates you may choose to implement a custom transport.
Once a transport is created you can then use it by adding it specifically to a configuration. This means that you easily can add several transports in the same server and let them use separate endpoints. All clients will still be able to communicate with each other if you want to.
Transports should not be mixed up with protocols. The transport just set the rules for data encryption/decryption. The protocol sets the rules for the format of the data.