I'm going to avoid RL examples and stick with post-scarcity 24th century. The people who colonize planets do so in order to have something to do. They work because they want to "improve themselves" as Picard said and Jake Sisko was made fun of by Nog. You settle Planet Alpha-Alpha Gamma because you want to have a town that's named after you and help do something productive so that in 200 years, a planet is a thriving colony and you built that. You probably hold Earthlings in justified (?) contempt for being a bunch of people who do nothing with their lives.
Then Starfleet shows up and all the 10-20 years of work you've put in colonizing a place is demolished and you're told it was for nothing. You're moved back to Earth. Maybe your neighbors are moved to Mars. All you've done is gone and every bond you've made is scattered.
Oh and it's because the Space Nazis get your world. Maybe you'd want to say, "No."
The Federation greatly misjudged the situation with the Cardassians and we saw how it all ended up with the Dominion War. The Federation believed that they could exert economic and political pressure to force them to come to peaceful terms but every time we see them, they're breaking a treaty or plotting evil. Because they're based on the Nazis. The Federation did successfully negotiate the surrender of Bajor and that's good but the Maquis got a bum deal.
But what I don't get is why the Federation thinks its their job to go after the Maquis. The Maquis have given up their Federation citizenship.
They are not the UPF's problem anymore.
FWIW, I imagine the UFP might have intervened in Maquis conflicts because: a) they felt that was preferable to letting the Cardassians deal with the colonists on their own, b) the treaty probably stipulated that the Feds would get involved at that point, and part of being the good guys is that you honor your treaty obligations even if the other side is being less than entirely good about honoring their side, and most importantly c) the whole point of the treaty was to avoid a war which would cost more lives, and treaty violations such as the Maquis arming themselves threatened just such a war.
If the Dominion hadn't entered the picture then the Maquis might have even gotten their own independent state in light of a weakened Cardassia, especially if they could become a Klingon protectorate or such. Once the Dominion became a factor though, there was zero chance the Maquis were going to retain any disputed planets.