I just discovered this thread (and just registered), and wanted to chime in; this is still on the front page, so I hope my response doesn't count as a necropost.
My reading of Ganondorf's monologue in
The Wind Waker is that he's trying to talk himself into believing that he's still the good guy. He doesn't give a darn what his enemies think, so long as they think it while running away; he knows that Link and Zelda will never be persuaded to do anything less than fight him; but he had always been pretty sure that he was Batman, until the gods drowned Hyrule to keep him, personally, from taking it, and now he's trying to rebuild his confidence in himself. His attempt to conquer Hyrule was never about his people (Nabooru is speaking out of the Gerudo consensus when she complains about Ganondorf, as shown by how Ganondorf and his most loyal followers are hiding in the Desert Colossus instead of operating openly in the Gerudo Fortress); but if his war for Hyrule had been about his people, he would have been a self-sacrificing martyr. So maybe he can persuade himself that it was.
(He's also trying to figure out why he tried to conquer Hyrule in the first place. Ganondorf is not exactly introspective, however much he broods over his wrongs.)
But if not for the reasons he gave, why did Ganondorf do it?
To start with, consider his personality.
The psychologist John B. Oldham has a theory that normal human personalities are less extreme versions of recognized psychological disorders; I doubt that this is true, but [this](
http://ptypes.com/aggressive.html) seems to sum up Ganondorf at least as well as [this](
https://www.16personalities.com/entj-personality) does. (The Oldham Aggressive personality profile continually talking about power is definitely a plus.) Also watch Ray Harryhausen's [The Golden Voyage of Sinbad](
https://en.wikipedia.org/wiki/The_Golden_Voyage_of_Sinbad), paying careful attention to Prince Koura; and read Pearl Buck's [Sons](
https://www.goodreads.com/book/show/40776308-sons).
(Yes, that Pearl Buck. No, I'm not kidding. Wang Lung's third son, who ran off to be a soldier towards the end of
The Good Earth, grew up to be an ambitious warlord, who spends the whole book trying and failing to conquer all China
because it's there. It hasn't occurred to him that this might make him the bad guy. It hasn't occurred to the narrator, either.)
Beyond his personality: Hyrule is very unforgiving with its enemies, but Ganondorf is a vassal of the crown in good standing when
Ocarina of Time begins, which suggests that he fought for the crown during the Hyrulean Civil War. Or at the worst, he stuck to armed neutrality, like he did in
Hyrule Warriors until Cia was defeated; either course of action feels plausible enough.
After the war, Ganondorf felt cheated of his rightful share of the spoils. Part of it was that he wanted all of the spoils, and would have felt cheated even if he'd gotten a fair share; but part of it was that the king stiffed him. Think about it: if you were a king, and one of your vassals was an ambitious, aggressive, magically potent, insufferably cocky ENTJ, and all the rest were aimiable nonentities, how much land and authority would
you give to the one guy who could potentially threaten the throne?
And even if Ganondorf didn't have Bad News written all over him, he would've been cheated for another cluster of reasons: Darunia was the king's sworn brother, the Gorons and Gerudo were feuding (wear the Gerudo Mask and talk to Darunia), and even if they hadn't been feuding there's no way Darunia and Ganondorf would have gotten along. From Ganondorf's perspective, Darunia was a dim-witted bro; from Darunia's perspective, Ganondorf was an arrogant pansy. They were just similar enough to hate each other, and neither of them was going to be the bigger man and keep their personal grudge from messing with the kingdom's politics.
So, after the Hyrulean Civil War, Ganondorf had a grudge against the king, against the king's sworn brother, and probably against Hyrulean civilization in general because it was more aligned with the king than it was with him. The Hyrulean Civil War had gotten him used to the idea of killing people and breaking things in order to get what he wanted; it might also have given him a case of PTSD. (His concept art in OoT was specifically meant to suggest that he wasn't quite all there.) He had a cadre of veteran warriors, loyal to himself and no one else, certainly not to the Gerudo as a whole. (Just ask Nabooru!) And he had a pair of demonic-shrine-maiden foster-mothers, who whispered to him about a divine artifact that could solve all his problems, put him on the throne, and incidentally get rid of Darunia and the Gorons in the process...
In this situation, all Demise's influence had to do was to make Ganondorf strong enough to get the ball rolling -- in particular, giving him the power to curse the guardian gods of the Kokiri and Zoras, even before he had access to the Triforce. But, in the absence of evil magic from before the dawn of time, I'm sure Ganondorf could have found some other way to kill the local gods when they didn't give him what he wanted. He's resourceful like that.