A terrorist is just a freedom fighter by another name. Whether he counts as a hero or a villain depends entirely on your point of view.
There's certainly overlap between 'Terrorist' and 'Freedom fighter'. The Maquis and the Bajoran resistance fall into that overlap.
Pretty hard to describe Terra Firma, The Circle or abortion clinic bombers as 'Freedom fighters'. Terrorists who fight not for freedom, but to force people to follow their own will.
You hit it pretty good. Terrorism in the end is just a method. A morally questionable one at best, but generally the only way a small group can effectively fight a bigger one in the technological age. Not all terrorists are freedom fighters or are even remotely interested in freedom.
The Maquis and Bajorans were certainly freedom fighters, along with Damar's resistance.