LR4: export folders to JPG, keeping structure
The plugin you mention works as a Published Smart Folder AFAICT, and in the linked page is an example showing how you might include images according to their Rating. However there are other possibilities.
If you want all images inside (say) a 2012 folder and its subfolders to be included, you would make that one of the criteria for the smart collection - something like, "Folder / contains / 2012" (perhaps you may add some other criteria as well, for example excluding images with the "reject" flag).
Then all the qualifying images will automatically appear inside the publish window, ready to go.