Referenced In-Universe in Bishop Barron's video on "The Limits of Tolerance." An Episcopal Bishop interpreted an exorcism in Acts of the Apostles as an act of intolerance against a demon who was charitably giving a slave girl unique spiritual gifts. Bishop Barron uses this absurd anecdote to distinguish an all-inclusive, never-challenging love with the Christian love that requires intolerance. That is, intolerance for Satan.
"Up until last month in Venezuela, the entire Christian interpretive tradition read that passage [...] as the story of the liberation of a young woman who had been enslaved both to dark spiritual powers and to the nefarious human beings who had exploited her. But not Bishop Jefferts Schori, who reads instead a story of Paul's deep intolerance."
The Nostalgia Chick and The Nostalgia Critic get this too, with some of her male fanbase treating her like she's a Closer to Earth goddess and a bit of his female fanbase treating him like he's a poor love who just needs a snuggle. Even though they are generally good people and she's a Broken Bird while he has issues up the wazoo, it's been made clear that they're both fairly douchey as well.
The Chick's bad side (always present enough for the fanfic writers to make her a Bastard Girlfriend) is coming out more with every video since "Kirk vs. Picard", in a attempt to make the difference between Nostalgia Chick and Lindsay Ellis more obvious. Doesn't stop the love, though.
In the same vein, there's Linkara. He has a big ego, is rather self-obsessed ("It's always great to see me", he says to his girlfriend's welcome), is often oblivious to things going on around him (such as Mechakara), and his number-one priority seems to be the size of his fanbase. Worst yet, he has a selective memory about some of the less-than-heroic things he's done (watch his later segments in Kickassia again after his big Badass Boast). You'd think these attributes, coupled with his desperate need to save people and be thought of as heroic Nice Guy, would be apparent; according to his fans, however, he's the nicest, most heroic guy on the site.
This was directly addressed in the "Guns and Sorcery" story arc, in which Linkara's magic stopped working because Margaret, the spirit in the Magic Gun, sensed he was turning evil (with many of the above examples cited as proof). His powers returned after he owned up to his moral shortcomings and vowed to try to be a better person.
A sort of in-universe example features Snowflame, from the New Guardians #2 and #1 reviews. In the first video, he's loved for being an extremely hammy and hilarious villain. A villain who kills people and deals in cocaine. When Linkara later reviews New Guardians #1, he has an actor portraying him on set as a lovable and overly energetic Cloudcuckoolander.
This can happen very easily with any instance of Alter-Ego Acting when fans don't realize that character and actor are not meant to be one and the same; for example, while Lewis Lovhaug is a very sweet, friendly guy, Linkara's an asshole and Lewis has openly said so (as he pointed out, what else can you call a guy who threatened a friend with spaceship-based weapons in order to win a petty argument?).
Hyper Fangirl gets considered by a lot of people as cute and adorable and her stalking victim Critic should just be nice to her. Even Doug himself complained about this.
This trope is a massiveBerserk Button for almost all of the sporkers at Das Sporking. Many of them express confusion, during their sporkings, about why the fanfiction writers fangirl certain villains at all if they're just rewriting them in ways that don't resemble their actual selves at all.
The Notebook and Tony the Talking Clock in Don't Hug Me I'm Scared have an unusual case of this. In canon, they're essentially Misplaced Kindergarten Teachers who browbeat and bully the main characters into accepting their viewpoints, and their "lessons" had a tendency to conclude in bizarre and brutal gorefests (how much of a hand they had in the gorefests is iffy). Neither one really demonstrates any personality traits beyond being self-obsessed and mean. In fanon, watch as they transform into the protagonists of a Tim Burton film and become kooky, quirky Comedic Sociopaths, playing up their association with creepy things and massively playing down their general rudeness. They're also usually made into love interests, even though they've never had any kind of interaction.
The Monstergirl Encyclopedia has this in spades. Many male readers reading about a setting full of hot monster girlsthat all want to have sex with men find the concept quite enjoyable, ignoring that the monstergirls will generally rape any men they see and force them into a relationship, commonly using Mind Control powers or simply superior force to make them stay. The Demon Lord responsible for the current setup is a Well-Intentioned Extremist that wants to end a Vicious Cycle of humans and monsters constantly killing each other at the whims of the Chief God, but the only way she could think of to override the monster's instincts to kill humans was to turn them all into lustful women that could only reproduce with human men. She's also spreading demonic energy over the world, which transforms the landscape and and turns humans into Incubi if male and random monstergirls if female while also brainwashing them so they aren't bothered by it. In addition to this, she's willing to eagerly convert/brainwash races that were fairly peaceful towards humans to begin with to strengthen her own forces. The Chief God's resistance to this presents of a risk of extinction for all races, due to fact it means new men aren't being born of the constant monstergirl/human couples, though the Demon Lord is trying to prevent this. Many readers will, however, miss the whole brainwashing deal and simply consider the Demon Lord a hero.
RWBY sometimes does this to Roman Torchwick and particularly, Neo. Roman is a thief who is shown to have no qualms in killing people of various ages, working with terrorists and even crash airships. Neo is his ruthless bodyguard that was already shown to have no issues with trying to kill a main character, support him in any attack or brutally beating people down. They are though, they seem to be the only villains who genuinely care for each other, with Roman sometimes being interpreted as Neo's Parental Substitute. They get a better treatment than the other villains in the series that did got a tragic backstory. It helps Roman is a suave thief and Neo is Cute and Psycho.
Raven Branwen is often treated as being a tragic figure who left her daughter behind to help her. Mind you, the woman has all but said she doesn't care about her daughter, is a bandit leader that kills entire villages either directly or by having the Grimm finish them off, is pretty petty and is despised even by her twin brother. It helps that she's the mother of one of the main characters, Yang, as well as being equally attractive as Yang herself.
The Slender Man sometimes gets this treatment, much to some people's horror.
There's a gag comic circulating explaining why he's not actually evil. For a start, he's only stalking you because he's trying to return that DVD he borrowed from you.