They left the Federation, but did not attack it, IIRC. Show them doing something downright evil would make it understandable, but for the most part it was self defense.
That's not true, the Maquis actions had the potential to reignite the war between the Cardassians and the Federation.
True, but the problem is in episodes like Pre Emptive Strike, they showed things like Cardassians sneaking into a human colony and then opening fire and killing innocent civilians.
Showing the Maquis in a sympathetic light like that, and then later branding them as villains that Starfleet and Sisko are obsessed with hunting down seems odd looking.
So it's not a surprise if some fans don't see the Maquis as villains. It's almost as if the show had to make the Maquis characters seem almost immoral, in order to justify the heroes of the show going after them.