Yes, personally I would be as reluctant to write a gay antagonist as I would be to write a black antagonist. However, the example from Johnny Silvercloud about 'Black Panther' gave me pause because the antagonist actually has a completely reasonable point of view.

Writing this now, I see I should have used "antagonist" in the title rather than "villain" because antagonist doesn't imply the character is evil. I think the more your work moves away from good vs evil and into the nuance of conflicting positions, the closer you get to literature. Thanks for the comment!