This question might be really stupid. They are both protocols, right? So what's the difference between them?
Protocol is a very generic term. FTP is a network protocol which defines how client and server interact with each other in order to transfer data. protobuf is instead a description how structured data should be serialized, for example in order to transport the data over a network but also to store the data locally.
Thus, FTP is more like a car traveling on the street while protobuf describes how you put all the various luggage in the car, how you pack your bags etc.