His misunderstanding is this: Humans don't randomly slay goblins just because they're goblins; humans attack goblins because goblins do things like sack Sapphire City.
Bingo.
Redcloak doesn't see himself at the villain, not really (he's admitted he has that narrative role, but seems to think it's undeserved), he sees what he's doing as a huge quest for justice for the Goblins and revenge for the goblins that the Sapphire Guard, commanded by Soon, killed to purge the world of the threat of the Gates.
The problem is, that the Goblins, as a whole, serve The Dark One. His master plan is to use The Snarl to hold all of creation, the world and all the Gods, hostage, to force massive changes in the world for the benefit of goblins (and almost certainly to the detriment of all other races and Gods).
The Goblins all serve this plan, unknowingly except for whoever wears the Crimson Mantle (unless they have completely left goblin society and renounced The Dark One). Now, they might not know the plan per-se, but goblins are a "usually" neutral evil race, so they have probably done a lot of other bad things they know about (remember, they were whipping human slaves just for fun during the occupation), and it's a safe bet to say they'd be cool with finding out their God actually has a secret plan to hold all of reality hostage so Goblins can rule the world.
The Sapphire Guard learned of this, and went on their crusade to destroy the Goblin civilization to prevent this plan from ever coming to fruition. What Redcloak saw as the unwarranted and unjustified murder of his people was actually trying to prevent the apocalyptic destruction of the world and/or gods.
Even when he had The Plan shown to him, he never pieced that together, he just jumped onboard with the idea of getting revenge.
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