A protocol, in the computer sense of that word, means the same thing as "a set of rules that everyone agrees on to use some particular type of software or hardware."
The best example is networking protocol, which tells you how to "talk" to another computer by defining what kind of message you have to send out of your networking hardware.
The International Standards Organization (ISO) has defined a series of layered protocols to cover certain situations. There is point-to-point hardware protocol, which defines how two hardware devices talk to each other. Then there is a way to put something inside that message to allow the hardware devices to carry information back and forth. Putting something inside a message is called encapsulation, and is a very big part of current networking protocols.
The most commonly used networking protocols form a "family" called Transmission Control Protocol / Internet Protocol (TCP/IP) and these very protocols are how your computer posted your question. (And how mine answered it.) This family includes things like File Transfer Protocol (FTP), SSH (Secure Shell), Hyper Text Transmission Protocol (HTTP), Dynamic Host Control Protocol (DHCP), and many others.
I have seen diagrams that reveal literally hundreds of protocols and layers, from the short-hop protocol used for machine-to-machine transmission all the way up to end-to-end protocols that take a single message through many hops. And there are more layers than that.
All of those layers use the same concept, though. ALL networking protocols indicate where they want to go and where they came from. They all have what is called a payload, which is described by a header segment (a sequence of bytes) in the overall message. If some form of encapsulation was used, that payload might itself be a message and the computer currently handing the protocol might just be a middle-man. The ISO model recognizes 7 general layers.