When you build a main character, they need strengths and weaknesses to really feel “real” or be interesting. They need flaws, even if that flaw is tied to their strength or virtue.
If you have a character whose primary virtue or strength is their combat prowess, or empathy, or bravery, or whatever, then making them of “average” intelligence is an easy flaw to give them. Not just because it makes the writer’s job easier, both for the bar it sets in conflict complexity and for easy conflict generation, but also because it makes it easy for them to make mistakes. It also makes them easier to empathize with as soon as you put a “smart” character into the mix to spout techno/magic babble and have them be exasperated or confused.
So if intelligence is such a valuable and easy flaw to put into a character, what happens if you make it their primary strength?
Well, you’ve got to weaken some other part of them. Take away their combat prowess or bravery and they quickly cease to be a hero. Take away their competence in whatever field is important and their intelligence starts to feel suspect.
But oh, hey, if you take away their empathy or charisma, now you have a “realistic” character with flaws and strengths! Sure, they’ll tend to be a bit socially clueless or weird, but that makes them quirky and amusing! Sure, they might become a bit of an asshole or arrogant, but that gives them a flaw for all the other characters to point out!
Hell, now the reader can even feel a bit smug: sure, they might not be able to play five games of chess from memory simultaneously, or whatever passes for intelligence in most fiction, but they’re at least people-smart enough to know not to be an asshole to their friends or family, or so socially clueless that they embarrass themselves constantly!
So we have characters like Monk or L, who are socially inept (mental disorders ramp this up in further empathetic ways), and House and Rick, who are assholes, and BBC’s Sherlock, who’s both. A smart, kind character isn’t hard to find as a friend or mentor figure, but as the main character it’s exceedingly rare, and without social awkwardness of some kind, even rarer.
There’s likely more to it than just this, some high profile real world examples probably influence the public zeitgeist, but in regards to fiction? It’s hard to really write a character that’s smart AND charismatic AND brave AND empathetic AND everything else they need to be relatable and a hero, without having a Mary Sue on your hands. So social skills and/or empathy are generally the easiest things to cut.
Additionally, seeing someone socially dominate others can be particularly cathartic if the “enemy” is considered deserving by the author/audience. Being able to embody one’s more misanthropic characteristics and puppet them around calling out the “idiocy” of the world around them feels good for people frustrated by that it in their day to day life.
We don’t get that catharsis/enjoyment nearly as easily or as often if the character is also nice, the way we tend to strive to be, or are told we have to be.