The problem is they never made the Maquis "bad" enough for the fans to understand the obsession with hunting them down.
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.
For the most part I think the fans think the Maquis were more foolish than evil because they choose to stay on planets they were previously warned were in dangerous dispute.
TOS, TNG made a point of saying the Fed is super prosperous. Colonization is shown mainly as a challenge not a necessity.
So I don't always understand the Maquis.