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.
They attacked the USS Malinche
. True, they didn't destroy
it, but they still attacked it.
is absolutely correct: the Maquis were poised to reignite the Federation/Cardassian war. Their actions were a direct threat to a very fragile peace.