A site is a location. The leader of a Zombie Army might remind his underlings: “Your web site is just a collection of pages at one address on the Web. Your burial site is where you find more soldiers!”
Site can also refer to a specific parcel of land, such as a building site or a burial site. Although a website has no physical location, it does have a virtual one, which is reached the same way a physical location is: by going to an address.