A notebook shared to Mathematica Online is like a document uploaded to Google Docs. It's stored in the cloud and can be accessed, evaluated, and read by a group of people. An object deployed to the Programming Cloud can have the same state, as a communally-editable document, but can also be a machine-readable API, a FormFunction, or a fully dynamic webpage. Mathematica Online is focused on providing access to Mathematica's notebook-based interface on the web, while the WPC is a true cloud integration.
Of course, I could be getting the whole principle of this wrong, so anybody is welcome to correct me. :)
