I'd rather use a different explanation than Marco:
A plugin project is what you add to the IDE - This is where your actual plugins live. Eclipse organizes around projects, and the projects are what makes up a plugin for Liferay. As the IDE interprets different kinds of projects in a different way (e.g. standalone Java Applications vs. "Dynamic Web projects" etc), a "Portlet Project" or "Theme Project" just adds to this list.
Once you have a plugin project (of type "Portlet") you can add as many portlets to it as you like. Thus, if you're developing portlets, you'll always have a minimum of one portlet plugin. This portlet plugin can hold any number of portlets.
You'll always deploy the whole plugin to Liferay - this fact might influence which portlets you want to group into a single plugin.