I can fully understand why Beltran was frustrated - his character was woefully underwritten and was basically shoved into the background in the later seasons. I can also understand why he stayed - it's still a steady paycheck, and besides, quitting a show might have hurt his chances of getting cast in future projects: "worked 7 years on a high profile show" must look better in one's resume than "quit the show because of disagreements with the writers/producers and dissatisfaction with the development of his character". I bet it's not that easy for most actors to find work, especially steady and well paid work, so he wouldn't have the incentive to leave unless he got a better offer. But despite the money, stability and relative amount of fame, it must be incredibly frustrating when you don't get to feel fulfilled by your work. Many people don't just work for the money, there is an a urge to be creative, to show one's skills, that can be far more fulfilling than the money.
But I think he might have done better if he hadn't given up and grown so disinterested in the role. There were many times in the show, esp. in later seasons, when he just didn't seem to be trying, and when he was wooden and indifferent even on rare occasions when he did get something to do. That kind of attitude might have only hurt the chances of the writers even trying to give him something to work with.
The wish for a "stronger" Chakotay character seems to be some mixture of a Vortaesque rage at seeing Roddenberryan humanism and the presumed necessity that Janeway be the only Trek captain to be showed up as a flawed commander. It's strange nobody every wanted T'Pol to be right against Archer, even though Archer was explicitly written to be a pioneer who would necessarily get things wrong.
Eh, what? Every Star Trek captain has been shown as a flawed commander, most of all Archer. Especially during the first couple of seasons, when he's shown to be reckless, naive, prejudiced towards Vulcans... T'Pol was right most of the time in that period, when it was usually her advice that Archer either ignored and got everyone into a mess (early episodes like "Strange New World") or, later on, when he actually listened to her, helped him sort out the mess or not make it in the first place. If anything, Archer was made a bit too obviously flawed, judging by the reactions of many of the fans who just couldn't get over it and called him an incompetent idiot.
You seem to think that playing against a strong character makes one weaker, and that the best way to make a captain seem strong is to weaken the other characters? I completely disagree. If TPTB wanted Janeway to come off as a really strong captain, weakening everyone around her was a bad way to go. Did Spock's strength as a character weaken Kirk? And having a bunch of strong, well developed characters on DS9 didn't make Sisko into a weakling. Character interactions only help to define the characters, which may be one of the reasons why Janeway is, IMO, the least defined of all Trek captains, and why her character and principles seemed to change according to whatever an episode's plot demanded. If she had had someone with well defined character and principles to play against, maybe she would be written with more depth and consistency than "a female Starfleet captain who is, like, totally awesome and badass".
And what the heck is "Vortaesque rage"?
Archer typically is shown as resentful and hostile toward T'Pol just for her being a Vulcan, and a lot of times she IS proven right when the two disagree, especially when she's advocating caution against Archer's inane impetuousness.
sonak, that
is the strange thing, that Archer is despised when the show portrays him as wrong against T'Pol, but Janeway is despised when shown as right as against Chakotay.
I can't remember when Janeway was shown to be right against Chakotay? I guess you could say Scorpion, but other than that - she was wrong in Equinox, as she admitted herself, and other times he was nothing but her yes-man. It's not an issue of whether she was right or wrong against him, the problem is that he hardly ever offered a different opinion.
Other Trek series have heroic captains without complaint. Sisko even gets to become some sort of rinky dink god without setting off fan BS detectors!
Funny, because I've spent many hours arguing just how bullshit the whole "Sisko's mom was a Prophet" thing was, in so many ways...
Regardless, Sisko was shown as morally ambiguous multiple times, what with his actions towards the Maquis, his obsession with Eddington, his actions in
In the Pale Moonlight...
Since DS9 consistently portrayed the Maquis as semi-villains (badass outlaws, terrorists and other such drivel,) however does this explain why some people wanted Chakotay to put Janeway in her place?
Erm, the Maquis
were terrorists and outlaws, as portrayed on every Trek show they appeared on.

I don't know how you could claim that they weren't portrayed accurately, since they, you know, don't exist in real life.
I don't know anyone who wanted Chakotay "to put Janeway in her place" (?), but I know lots of people, me included, who wanted Chakotay to show some sort of personality, attitude and some opinions of his own, instead of doing nothing but smiling and chatting with Janeway on the bridge and being basically useless. He doesn't have engineering or piloting skills so his whole purpose was as a former Maquis leader who becomes Janeway's XO. But the writers ignored the Maquis part almost completely, which makes you wonder why they even bothered introducing it in the first place; the Maquis started wearing Starfleet uniforms and blended into Starfleet after the second episode, there were barely any tensions or anything to distinguish them from the rest of the crew, and Chakotay himself immediately started acting like a good Starfleet officer. There were just a couple of occasions when he offered any kind of different opinion to Janeway; one of the rare examples is
Scorpion, indeed his finest hour; but the other one,
Equinox, where he had an excellent reason to oppose Janeway (and was right, according to her own later admission) resulted in him caving in because, as he said, "it wouldn't have been right" for him to stage a mutiny. It wouldn't have been right? Spoken like a true rule-abiding Starfleet officer.

This guy used to be a Maquis leader, for heaven's sake!
Claiming that Chakotay couldn't be credible as an (almost) equal partner in decision making just because he was an ex-terrorist/outlaw is utter nonsense, especially as Voyager was in the Delta Quadrant where Starfleet was not in a superior position, with legal and governmental support. If anything, the fact that Chakotay had been portrayed as someone who had resigned for Starfleet and joined the Maquis, indicated that he was the kind of man who was willing to fight for what he believed in, and that he was governed by his own moral principles rather than Starfleet rules and regulations. Which is why his attitude in
Equinox didn't make sense and was another reminder of just how utterly wasted the potential of his character was.
I wouldn't have wanted him to be a jerk, and he didn't need to be one to be interesting. He could have been written as stoic, but determined man of strong convictions, who gradually (not at once) becomes deeply respectful of Janeway, but, instead of being a useless yes man, is ready to present opposing views and another perspective that comes from an ethical code that is different from Janeway's Starfleet principles. Also, his spirituality and background needed to be written as something other than utter nonsense.
It shouldn't have been that difficult. After all... you know that Trek show that started a few years before VOY and was still on the air at the time?

That one proved that an ex-terrorist, non-Starfleet, opinionated, deeply spiritual XO on a Trek show can be a strong, complex, well developed character who carries many strong storylines and grows enormously during the course of the show.
If one wants to rebut by noticing that the Vulcans and the Maquis were semivillainous in different ways, refer to the part about the Vortaesque rage at Roddenberryan humanism.
I have no clue what you're trying to say, especially since I still have no idea what "Vortaesque rage" is supposed to mean.
All I get from this is that you seem to be stuck in the "heroes and villains", "Starfleet good, outlaws bad" mode of thinking. By mid-1990s, after the late seasons of TNG and DS9, Trek had, IMO, became a bit more nuanced and layered than that.