I feel like LoZ lore and the way it tells its stories encourages the mindset that one side has to be completely in the right and one side has to be completely in the wrong. The wrong side, as a result, becomes a plot device that amounts to "needs to be annihilated" without really encouraging examination of why they are considered wrong.
There is also this idea that LoZ antagonists are fanatics and extremists who have a rigid mindset versus the LoZ protagonists who tend to be framed as being more open-minded and understanding, and I also think this is untrue of canon. LoZ protagonists tend to speak in very certain terms about how the antagonist should be viewed i.e. they are vile, they are monsters, they cannot be reasoned with. There is really no serious attempt from either side to come to an understanding of the other, of why they do what they do. There just is no nuance. Link and Zelda, and Hyrule at large, will only show kindness and understanding to people they have deemed worthy of it. As soon as you are deemed unworthy, that door of mercy is shut. Personally, I find the study of both sides of extremist thought to be fascinating. How would someone who has been trained to view the Yiga as nothing but troublemakers and cultists that are the scum of the earth learn to view them as human?
To be honest, it has been troubling to me to see this sudden rise of people demanding that they want villains that are just evil because they don't want to feel sorry or understand the villain, that "some people are just evil because they can be evil" and then point to the rich and fascists like Trump and Hitler as examples. And it is funny to me. Do people think people like Trump and Hitler were born evil? Did their circumstances and upbringing not enable their worst impulses and ideas, and reward them? This isn't about feeling sorry for them, this is about understanding why such people exist and believe they can do what they do with impunity. This idea that discourages examination of people and thoughts that makes us uncomfortable because we just want to view them as "pure evil" so we can dunk on them and kill them without a second thought really goes hand in hand with the rise of fascism.