In One Piece, there's Brook, a skeleton. Even after his death his afro remained due to having "Deep roots". His hair is actually a plot point as, being an skeleton, he will be no longer recognisable to the whale he met 50 years ago except for his afro; due to him being an skeleton, it won't grow back if damaged. He does anything he can to protect his afro.
There's former Fleet Admiral Sengoku, though you rarely see it as he wears a hat. He leads the Authority Equals Asskicking Marines and later shows that he ate a Devil Fruit that gave him the ability to turn into a giant golden Buddha-like moving statue, afro and all.
Misty Knight and Monica Rambeau from the Marvel Universe. Whereas Monica has updated her hairstyle each decade, Misty's afro is so iconic (she was Marvel's answer to the Blaxploitation craze), she has kept it up to the present day.
Samuel L. Jackson's character in Pulp Fiction, though technically his hairstyle is a Jheri curl.
It was an afro in the script. Apparently they tried dozens of afro wigs and couldn't find anything they liked. They tried the Jheri curl last, almost as a joke, and decided it was perfect. Which makes this, when you think about it, a subversion.
Jackie Brown is another Tarantino subversion, given that the movie is Tarantino's blaxploitation homage.
Miror B. from Pokémon Colosseum has a gigantic afro modeled after a Pokéball. He's also a Cipher Admin in the first game while he's a wandering thief in the sequel who captures the Pokémon you fail to snag.
Andrei Ulmeyda, killer7's Badass Normal, wears an afro. Later becomes his weak point after turning into a Heaven Smile and killing all members of the military in the area with his acidic blood. And he has the chance to One-Hit Kill you.
Saturno, one of the more balanced competitors from Capoeira Fighter.
Kid Quick and Title Defense Disco Kid in the Punch-Out!! series.
Todd, the butler of the Schrodinger Family in Wild ARMs 3 has an afro. Unlike most examples of the trope, it is to your advantage to attack his hair; by setting it on fire, it will deal him Damage Over Time.
Subverted by Afro Ninja, a popular viral video where the man attempts to show his asskicking skills and fails miserably.
Double subverted when you figure out this guy is a total badass, missed the stunt only because of jet lag, and after resting up, got the job.
And in the movie based on the viral video, he certainly does kick some ass.