I just watched the episode in which Chakotay is brainwashed into becoming a soldier for an alien group. I can't remember the name but it's in Season 4. Anyway, he tells the other soldiers there about his attitude to killing and fighting (i.e how people where he is from think about the enemy, killing is last resort etc.) which seems totally at odds with how a terrorist/freedom-fighter group would think. The Maquis were named after the group of French Resistence fighters in WWII and you can be sure none of them would have Chakotay's attitude to killing.
The episode is "Nemesis". I thought it was one of the better Chakotay episodes.
Also the Maquis COULD be considered a lighter equivalent to the Bajoran Resistance fighters who killed many Cardassians as well (however, the Bajorans were somewhat way more justified). If someone tried to take over my state or country, hell yea I would be pissed too. But, of course, killing is the last resort. Especially if you are a "peaceful" person.
Also liked him in "Unity" where he has mental orgy with a group of ex-borgs.