Why is the Captain's word absolute?
The tradition that a Captain's word is supreme on his ship is a naval tradition. It is weird. I was never in the navy, but it was explained to me like this: because the ship is an island unto itself, cut off from everyone and anything for vast stretches of time, the Captain's word needs to be final. Things simply do not work otherwise.
It is the Captain's job to interpret orders from higher command they receive, and to carry them out. Nobody else on the ship questions the Captain. Indeed, if the Captain disobeys orders from Navy Command, it is not the job of anyone on the ship to remove them. They will be removed the next time they make landfall, and a new Captain will be installed.
This is true even if a higher authority is already on the ship. Technically an Admiral cannot overrule a captain on the captain's own ship. The Admiral could fire said captain, and attempt to install a new one. I am told that any such attempt would run into a practical problem that said Admiral would have difficulty finding an officer willing to play along.
Implications for generation ships
These concerns will be far more pressing for a generation ship. Generation ships will not be able to maintain radio contact for very long. Relatively quickly they will be out of range. After a few last dumps of mail (light lag means conversations won't really be possible anymore) the generation ship forever loses all contact with its parent culture. It will be alone forevermore.
The Ark theoretically could fire probes back Homeward with ship's logs and status updates; but nothing from Home will have any realistic chance of intercepting the Ark. This is likely a fools' errand anyway: generation ships are fire-and-forget. Fuel and materials spent on such probes is a waste of good resources (which will be tight).
For all intents and purposes, there is no longer any higher authority. And there will be constant threats to the life and safety of everyone on board. Things will constantly be breaking down. Naval vessels can pop into drydock when they need to perform major repairs. Generation ships have no such capability.
A generation ship will be a maintenance and logistical nightmare
Generation ships will need to have components with a very long lifespan. They will also need the ability to manufacture new components. And things will constantly break down anyway. An army of support staff will be required to keep everything running. This staff will need to be replaced with new staff.
The logistics of keeping everyone well supplied will be equally challenging. You have what you have, and that's that. If something isn't already on board, you either make it or you do without. And no matter how well you plan, there will never be enough. People will like that just as well as they like it here on Earth.
A revolution probably results in catastrophic mission failure
Order must be maintained on the vessel, at all costs. One person going postal on a generation ship can sabotage key equipment in a way that can't be quickly repaired (or possibly even repaired at all) and the mission is fucked. Possibly life support is also fucked, and then everybody dies.
One way a revolution succeeds is by causing trouble (or exacerbating existing trouble). Then you just watch the resulting firestorm bring down the old regime, and waltz in and take over. That's bad. A violent takeover is also bad, because of the high likelihood of damaging the ship or killing the only people who know how to fix the ship.
Military discipline keeps the ship together
For all the same reasons military discipline keeps things running smoothly in other contexts. This forms a stratocracy with the Captain as monarch. The ship is its own sovereign nation; its political development can be guided by the Founding Builders, but they will ultimately be responsible for its development.
No nation has ever been stable long enough
World history reveals that literally no country has ever been recorded to survive longer than several hundred years or so without some kind of civil unrest. Some parts of the world have yet-uncontacted tribes mostly left to their own devices; they might have been around longer. But nothing large enough to be called a nation has been static for that long.
And that's a problem, because a generation ship is a small nation. I really don't see any way around this other than military discipline.