I have a character who's got a controversial trait that honestly I'm a bit on the fence about. His name is Victor Cros, and he'll be playing the supervillain/mastermind/antagonist/whatever flavor you like role. A bit of background: He's an arrogant genius and a madman, he believes himself to above all others due to his intelligence and strong supernatural abilities. After a couple bad acts, he and numerous other supernatural inmates have been sent to a remote island prison to be observed. When he's introduced in the story he has a grudge against one of the protagonists, Evelyn Shields, an African American woman. His grudge isn't just because she's black, but it actually stemmed from the fact she consistently beats him in chess, which he perceives as an ultimate battle of minds. Losing in a battle of minds, not just to a woman, but to a Black woman, makes him completely indisposed toward her and he attempts to veil his numerous jabs at her being a woman and Black under a sophisticated dialect to save face. Which irritates Evelyn to no end leading to Victor being reported for harassment, alot. But me being Black myself I often feel like this subject may be a bit much. I mean villains are supposed to be assholes but Victor and his jabs Evelyn always seems to bother me the more I write them. And it's all because he wants to feel superior to her! It makes me mad because I know of people who are like this. My question is should I keep this trait in Victor's character even though it really makes me uncomfortable? And a bonus question, have you ever had a character that actually got to you like this?
Won't that make the reader feel the same? Thus laying your villain as hated; exactly what you intended to do? I say good job. I normally struggle because I tend to make slick villains whom I tend to like. Yes, perhaps not as much though, I created a monotheistic cult as the thorn for my heroine in the novel I'm currently writing. Their leader is the evangelical, belief blinded type who commands a great deal of power - Amongst the things I hate most in our world... But she'll get him, and get him good. So I don't mind so much.
...if that's how you want this character to come across to readers, then why take it out?... the point is, as you noted yourself, there are many people like this in real life... so why gloss over reality in your novel?... ...i've created a number of totally despicable villains... it never bothered me to write them realistically, although some of the things i had to have them do certainly made me cringe...
The thing about despicable villains is that it is thrilling to the reader when they are defeated. That's why we make them despicable. Is it the character who makes you uncomfortable, or the fact that you, a person whom (I'm guessing) your character would regard as inferior, have created him for the purpose of being taken down? If it's the latter, you need to decide how committed you are to writing the story. Whatever you decide, it should be what you think, not what anyone else thinks. All that said, I happen to think it's a compelling idea.
If your character is getting to you so badly, the odds are, they'll get to readers that badly, and that's a good thing if you're going for a completely despicable man. I'd say, stick with it and let yourself get angry with him.
If you feel that you are comfortable, I think it would be good for you to continue, because it causes your reader to root for your protagonist even more. However, if you do not feel comfortable with it, then by all means stop.