Comparing X-Files to Star Trek is like comparing Buck Rodgers to Supernatural
There are differences, but X-Files proved that an ongoing story can work in a TV show.
Chakotay destroyed their ship, remember?
So they had no supplies, no food, no place to sleep & no weapons.
Someone honest is offering them all of that and more as long as the do an honest days work...........and this person still needs to gain you're trust?
They were never treated as political prisoners or enemies. Why bite the hand that's feeding you considering you have no other options?
You're 75 thousand light years from home with nothing to your name. What's more important, your political views or a hot plate of food? Isn't that more believable?l
Just because Chakoty and the Maquis don't have much of a choice doesn't mean they have to be happy about. There should have been more resistance and push back against Star Fleet regulations and frankly I think a lot of the Maquis would blame Janeway for being stranded in the DQ. What's the point of having the Maquis on the ship if there is not going to be any conflict? It makes Janeway look like a total Mary Sue if all those Maquis people will simply defer to her right away.