I've been thinking 'bout this ever since the first episode. The good/bad guys role changes in different Arcs.
That's what makes it so good. We have Pirates vs Marines, and the obvious choice would be to say that Pirates are bad and Marines are good. But over the course of the story, we see that those tittles mean nothing, and that each individual is either good or bad, even if he is labelled a Pirate or a Marine.
I can be more precise. Basically, the World Government is the Law, and thus it is the Good. Since they are the law, everyone that opposes them are Bad, and thus, every Pirate, being them criminal or not, are the Bad guys. But the fact is, the World Government isn't always right, and there is corruption inside, and thus we see things that divide our moral consciousness. So we see Pirates that, despite being pirates, are actually good, and we see corrupt marines, that are suppose to be good, but are bad, all the way to deeper corruption and doubtable decisions made by the government many years before, which you'll see once you get to more advanced chapters (I don't want to give you any spoilers)