Its quite sinple really. A repository contains a set of stores. And each store contains nodes, associations and other stuff like acls. You will find people talk about "the DM store" but I find that unhelpful, DM does not have a unique type of store, its a higher (application) level concept.
The "protocol" is really just a name for a type of store. Someone in the early days of alfresco thought to make the store identifier look like a URL and that's the format used forever afterwards.
There are different types of store, for example there's the workspace stores which contains the files and folders you work with, the system store that contains "system" nodes, the archive store which contains archived nodes, the MT stores and the avm stores which contain avm nodes.
Alfresco Enterprise has the XAM store and Caching Store as well
There could have also been an "RM store" with the extra RM security although AFAIK that's not the way it was actually implemented.