The idea IS that Ganondorf's ethos had a point but he was also:
-Corrupted by power
-Cursed by the narrative because he is the incarnation and psuedo-son of the Anti-Christ and cursed to be evil no matterwhat
-A massive hypocrite who was reasonably ALWAYS full of shit no matter how revolutionary he sounded
When he takes over Hyrule, he:
1. Had Twinrova brainwash Gerudo warriors
2. Left them in the desert w/ a broken bridge
3. Never relocated them to Hyrule Castle Town
His Wind Waker speech was all an act, he never cared. The Gerudo celebrating his defeat in OOT says a lot.