Mike, it's simple.
Windows is like a Cessna 182. A fairly robust aircraft with not too many vices. It's a bit overkill to train on, suitable for a lot of applications, and sometimes wanting.
UNIX in general comes in many flavours. From relatively small (think Gippsland Airvan) to very large (A380), each fit for a specific purpose but too expensive to do much else.
Linux is like the experimental/homebuild/kitplane scene. It's intellectual capital consists of a large number of publicly available plans and parts, and you pick a distribution (Red Hat, Ubuntu, SuSE, Debian) that suits your needs best by offering the best combination of plans and parts you need. Like you would choose between a pre-assembled Jabiru, Europa, RV, Glasair or something else. Or you assemble it yourself from the component parts. Compared to the Cessna 182 they do require some more knowledge and skill to operate but the end result is more suited to your problem.
WINE is like putting the controls and operating characteristics (the "API") of the Cessna 182 in the cockpit of your hotrod kitbuild airplane. It's useful for those pilots (read programs) that only know how to fly Cessna 182s (read run on Windows).
VMWare (and others like MS Virtual Server and Xen) is like taking an Airbus A380 and putting a Cessna 182 inside of it, giving it its own airspace, air traffic control, runways and everything. This means that a Cessna 182 pilot can buzz around from the front to the back and generally have a good time, without impacting any other airspace users, while you take the A380 somewhere else.