The new AP stylebook makes 'website' one word, instead of "Web site." "Common usage" was the reason for the change. High time. They need to drop the capital in "Web" and "Internet" as well. When I was a mild-mannered journalist at a major metropolitan news site, the argument was that internet and web be capitalized under the view that "there is only one Internet, and only one Web, so these are treated as proper names." I argued (and argue) that the internet, and its appendage the web, are media -- like television and radio -- not discrete items, and so should be treated in that way -- no initial capitals. You watch television, not Television (unless it's the band), and you listen to the radio, not the Radio. You could couch the debate in terms of individual infrastructure elements, like a transit system - not a far stretch - but it still doesn't fly. In New York you take the subway, not the Subway (unless you're getting lunch).
My boss shut me down, of course, pointing to the conceptual stone tablets that spelled out how we... well, spelled things out. And now one of those stone tablets has been re-carved. Usage rules should and do evolve to meet the way things are actually used.