I see folks coming from two different viewpoints:
1. It's based on the concept coming from light skinned dominated countries that darker skinned people carry inherently negative/lesser traits (and/or light skinned people carry inherently positive traits) and therefore are easier to convey as villanous.
2. Based on how we have evolved biologically and as a society, we have placed different values and characteristics upon different colors. Light brings us life and understanding. Good. Darkness brings us chaos and death. Evil. Hence our cultural, mythological, and religious tropes.
I would argue that the foundation lies in view #2 (and for most cases it remains with #2) but as someone already said, some cultures/myths/religions have used view 2 and applied it to view 1 (dark is bad, so therefore darker skinned people are inherently more bad (or even less human) than light skinned people). This viewpoint is obviously wrong and needs to be fought. That said, I don't believe that view #2 is inherently malicious. Id say that the problem lies with our tribal natures applying values to outside groups [based on biological factors, groups based on ideas can still be argued against/opposed in some cases] that needent be applied at all.
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All that said, the video creator has made it clear that creators should not make villains dark skinned (evil smile, red eyes, or grey skin instead). I would also greatly argue that this sort of censorship isn't the right way to combat this issue. Someone argued before that perhaps a greater chance to see darker skinned heroes/protagonists would have a healthier and more creatively positive impact, and I'd agree.
A creator (whether it be film, novels, gaming, or any other media) should still be able to have a lighter skinned protsgonist and a darker skinned antagonist (and vice versa) as long as it's done tastefully and without trying to pin negative (or even positive at the others expense) connotations based on the color of ones skin.