Most importantly, all sites use the same protocol, http, or hypertext transfer protocol, which puts constraints on them that force similar structures. That's behind the scenes, where most users never venture. On the screen, web pages are as dissimilar as rooms, web sites as dissimilar as buildings. Yes, all the rooms have walls, floors, and ceilings, but they're decorated and furnished and populated very differently. A person's experience in a room is another level of structure.
People form mental models of the rooms in a building.
When you go into a building for the first time, you form a mental map of how to get from one room to another. If you spend a day or two, you quickly adjust your map to be more accurate. In that sense, there are as many different web sites as there are people clicking around in them. Many sites also have site maps, usually list of pages, but they may be color-coded or even arranged according to some metaphor. For example, Ricci Street uses a geographic metaphor for top-level navigation.