What PlayOnLinux does is simply make the process of installing programs through Wine easier. It helps you choose the best settings, Wine version, etc. to run your program as well as they can on your GNU/Linux distribution. Wine can be used on its own, PoL cannot; it's kind of an add-on.
Disclaimer: I'm a noob, not a dev; my advice is only a guess.
Attention : Je suis aussi noob que vous, prenez mes suggestions avec un grain de sel ;)