The difference between Mathematica online and the Programming cloud is partly in the interface. If you compare interfaces you find the Mathematica online interface missing menu items like: Deployments, Reports, creating New javascript, xml, css and html files, Create testing and template notebooks.

This is all about the -interface- and not really important since we address our cloud kernel by sending it expressions. It's more important to look from the viewpoint of functionality. Then the programming cloud and Mathematica Online are about the same. The only difference I know of is that you must have a producer plan to run the DocumentGenerator.

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. :)