Protocols and methods are both defined ways of doing things. However, there are some key differences between them. Basically, a method is much more rigorously defined than a protocol.
A protocol is a set of rules for a situation. So, an example of social protocol would be "keep your elbows off the table." It doesn't define where you should put your elbows when eating, it just defines one area where you should not put them.
A method, on the other hand, is a rigorous set of rules. If social methods existed, the above example would be much longer--"sit at the chair in front of the table with your feet facing forward, hold a fork with your right hand, resting your wrists on the edge of the table in between bites."
A protocol is used in areas where the user can make decisions on his own; rather than follow a set of rules, he just needs to know some loose guidelines, which he can base his actions around. Methods are used for more complex activities such as squatting heavy weights, wiring circuit boards, cleaning industrial equipment and other activities that require specific steps to be followed in a specific order.