Hugo Strange thinks Batman is The Übermensch and wants to be him. Unfortunately, Strange doesn't actually understand Batman's underlying motivation, and misunderstands it as a drive for power. He just ends up projecting his own thirst for power on the identity of Batman and makes himself try to usurp it.
In Batman Eternal, Jason Bard lost his lover/partner in Detroit because a Batman wannabe ruined a drug bust. Bard thus assumes that, like the copycat, Batman is just in it for the fame and glory and hates him. Bard also assumes all the other cops in Gotham hate these masked vigilantes as much as he does and will be happy to get rid of Batman. It takes every cop literally walking out on him for Bard to realize how they trust and admire a man fighting crime and Bard is in the wrong.
The Riddler isn't as bad as most of Batmans Rogue's Gallery, but his deep-seated need to be recognized as the most intelligent is the only drive he understands. Despite being the villain with the most social competence AND most attempts at reforming, he just can't bring himself to form normal human bonds that aren't decided by intellectual dominance.
This is a recurring motif in some Batman books; because most of Batman's villains are insane and because he's a very mysterious figure to most of them, whenever they attempt to deduct his motives or identity they'll often project their own issues and flaws onto him. Whenever any of them discuss Bats, it quickly becomes clear they're talking about themselves.
In Detective Comics (Rebirth) #980, Brother Eye is striking at the various team members but leaves Spoiler and Cassandra Cain alone. It then shows images of the pre-Flashpoint timeline where Cassandra was Batgirl and Stephanie was Robin and Batgirl herself. Eye states that "you are not your best selves" and "you will never measure up." Instead of being totally demoralized, both Stephanie and Cassandra laugh and embrace to Eye's utter confusion. Stephanie states that seeing there's a world where she was good enough to be accepted as Batgirl reminds her how strong she truly is and using it to take on Eye. All Eye can respond to their reactions? "Error. Error."
In one of the earliest stories told with the Corrupt Corporate Executive version of Luthor (in Superman vol. 2 #2, 1987), he notices that Clark Kent has some kind of connection with Superman and sets up a research project to find out the nature of the connection. When the researcher concludes that Clark Kent is Superman, Luthor fires her and scraps the project... because, to Luthor, it's impossible to believe that someone with that much power would want to "waste" time occupying such a humble persona.
As a general theme, Luthor understands that the CONCEPT of good exists, but doesn't really understand its basics, and seems to mostly confuse it with a mix of dominance and dependency.
It comes around full circle in The Black Ring. After achieving godhood, Luthor starts torturing Superman, thinking that he only pretends to have human emotions. When Superman provokes Luthor to delve deeper and watches Jonathan Kent's death, Luthor puts two and two together and promptly flips his shit because the alien got to have loving parents and he didn't.
Another early Byrne story had Superman stopping a disgruntled employee from killing Lex with a bomb. Lex assumes Superman set this up to rattle him as it makes no sense for Superman to save someone he knows hates him.
In the original Silver Age "Death of Superman" story (Superman vol. 1 #149), Luthor sits smugly through the Kandorians' trial, confident that he can bribe his way out. When asked for his plea, he answers that he is guilty. However, if they let him go, he will work out a way to restore them to full size. Luthor is taken aback when the judge retorts that "we of Kandor do not make deals with murderers" and orders him sent to the Phantom Zone for all eternity.
In All-Star Superman, when Luthor gains Superman's powers, when looking through Superman's eyes and how the universe is interconnected, he realizes why Superman was so benevolent. So much so that he completely atones and accepts his death sentence. In the same comic, Luthor goes full Smug SuperDumb Muscle when he obtains superpowers, implying his loathing of Superman is based on the idea that if he had those powers, he would be that person he hates so much.
In the Silver Age origin for Luthor, his first response to Superboy accidentally rendering him bald when the superhero put out a lab fire was to create grandiose public works projects around Smallville to steal Superboy's thunder as the local hero. However, Lex can't get it through his head that Superboy does not mind in the least; he's simply glad that if his former friend is carrying out them as part of a vendetta, at least he is doing it constructively. Of course, each project goes dangerously out of control, forcing Superboy to intervene to avert disaster and Luthor can only rationalize that Superboy did that to humiliate him.
At the end of "Superman's Phantom Pal", Superman explains to the villainous inhabitants of the Phantom Zone that Jimmy Olsen didn't give in to the temptation to spy on his Secret Identity because of the boy's "loyalty and honor." He then finishes up his speech by mentioning this trope.
Manchester Black kicks off a massive plan to destroy Superman, including appearing to kill Lois Lane, all to prove that Superman can be a killer just like Black. Holding Lois' body, Superman vows he will find Black... and then put him in prison for the rest of his life. Black is absolutely shocked that even the murder of his wife can't push Superman to go over this edge. He reveals her death to be an illusion and then takes his own life as he finally realizes that no, not everyone is a monster, it's just Black.
Black: You... you're not afraid of me. You... really do believe all this. Bloody hell, I didn't think someone like you could exist.
At one point, the d-list Batman villain the Ratcatcher attempts to murder someone. When Superman shows up, Ratcatcher screams, "This has nothing to do with you! Just let me kill this man and be done with it! What do you care!?" Superman simply replies, "I care." before taking him out.
The eponymous heroine hated Cat Grant because Cat published news articles slandering her. Still she rescued Cat when the villain Dollmaker kidnapped her in the 2011 story arc "Day of the Dollmaker". Dollmaker couldn't understand why Supergirl would want to save someone she hated.
Belinda: You think you're so important! You think you're the center of the universe! Supergirl: Uh... Not really. Belinda: You totally do! I'm you and I know what you think! You act all sweet and nice, but inside your head, you're an arrogant little angel prancing through the sky on a stupid magical fantasy horse, acting like you're better than everyone!
Like Brainiac, the Joker, and Lex Luthor, Darkseid has this problem. He really can't comprehend good. Justified since he was born evil and grew up surrounded by nothing but evil. Darkseid honestly thinks that sometimes letting his enemies live a life of free will is a punishment, as he even turned Young Justice's Secret back to a normal human girl as a form of this once she betrayed him. But he missed the fact he was actually giving her exactly what she wanted in the first place.
The application of this varies, of course. The Suicide Squad earned this once he realized they dared to invade Apokolips, but the survivors were pretty much made of Survivor Guilt from then on, most notably with Amanda Waller, who's become borderline suicidal with some of her risk-taking since. Similarly, in the DCAU, this is Darkseid's vengeance on Superman at the end of his series, with implications that humanity never wholly trusts Superman again. Unlike in mainstream continuity, this does last in DCAU, and leads to one of Superman's closest friends in his series to join Project Cadmus in JLAU.
Both averted and played straight in Grant Morrison's JLA: Earth-2 graphic novel. In an alternate universe where evil always wins and good always fails, the Justice League realize that the only way to defeat Brainiac is by walking away in the middle of the crisis. Played straight in the way Brainiac really didn't expect them to do it, and is punished harshly when the 'evil' Justice League return home.
At one point when the Crime Syndicate of Amerika infiltrate the universe of the Justice League, Johnny Quick and Power Ring change costumes and pose as their heroic versions (The Flash and Green Lantern respectively). Almost losing a fight to supervillains, they are absolutely bewildered when civilians rush in with clubs to help them. When asked why they did this, the civilians said that they owed them for all the times the League's helped them. This prompts Power Ring to complain:
The New 52 version of the Crime Syndicate, introduced in Forever Evil, is also perplexed by the idea of justice. But unlike the original take, where those who were heroes here are villains in Earth-3 and vice versa, Earth 3 (without the hyphen) is an entire world (or should we say universe) where heroism, justice, and the basic good are considered foreign concepts. This Earth 3 mainly runs on survival of the fittest, where the weak are considered useless, and thus, don't put it in their minds to help the innocents. Even those who nominally should be the heroes are Well-Intentioned Extremistsat best.
The Wizard, long-time foe of the Justice Society of America, had this as his motive in his first appearance. He'd missed the early years of the team as he was in isolation, learning black magic, and when he returned to civilization, the Wizard could not believe that smart people with superpowers would use them for altruistic purposes. Therefore, the JSA had to be pulling the biggest scam ever, and the Wizard demanded to be cut in.
Some demons trap Traci 13 in a Lotus-Eater Machine where she is the uncontested ruler of the world and her father is dead. They are baffled when she rejects the illusion and wants her father back. She thought her father was annoying with his uptight refusal to believe in magic, so the demons assumed she would be happy with him gone.
In the DCcrossover eventUnderworld Unleashed, this ends up costing Neron badly when he reveals that his stream of deals with various DC villains and heroes was done solely to get Captain Marvel to cut a deal with him. Unfortunately, Neron thought that the Big Red Cheese would ask for something selfish. Instead, Cap asked for something completely selfless ("Let everyone else go and I'm yours."), which meant that when Neron tried to take Cap's soul, it burned him so badly that he fled. Neron gets similarly burned when he buys the love between The Flash and Linda Park. It causes him to start developing feelings for the souls in his possession, and he doesn't understand why. He ends up giving it up in disgust.
During the John Rogers run of Blue Beetle, Eclipso hits Jaime with a spell that will bring out his "deepest desires", which it believes will be some sort of dark, violent power fantasy. What Eclipso gets instead is... a dentist, as what Jaime really wants is a career that will make enough money to provide for his family.
The Queen of Fables thinksWonder Woman is Snow White and Superman is Prince Charming. She eventually discovers Superman's secret identity, and is unable to comprehend why "Prince Charming" would marry a "peasant" like Lois Lane instead of royalty like Snow White or herself. She also doesn't understand killing people and causing destruction just to get his attention won't get him to fall in love with her.
The Legend of Wonder Woman (2016): Zeus cannot comprehend why Diana would dare defy him after he offered to reunite her with her mother, in exchange for Diana becoming his champion and helping him kill off almost everyone on earth and then brutally subjugate the remainder, forcing them to ritually sacrifice each other for Zeus and the other Olympians to ensure they'll keep their power and not fade away. He doesn't seem to even realize that she finds his plans horrific or distasteful.
Watchmen: Rorschach isn't exactly evil, but he's still a brutal, criminally insaneVigilante Man. At the end, when Nite Owl, Silk Spectre, and Manhattan listen to Veidt's argument and realize that revealing his crimes won't save anyone, but will only jeopardize the peace that might come about as a result, Rorschach assumes that they're only joking. He doesn't believe that any superhero would let a villain go unpunished, even if it might be necessary to prevent The End of the World as We Know It.
A key reason the Mad Thinker is constantly defeated is because, despite all his genius and amazing ability to predict things in advance, he still fails to calculate how people will react differently than he expects them to in non-selfish ways. He even lampshades it at times with how things like empathy and self-sacrifice create a "margin of error" in his plans.
Doctor Doom gets hit with this in the storyline where he saves Reed and Sue's second child. His price is that the baby girl must be named after his lost love, Valeria. Doom, a hardcore egotist with a compulsive need to be the best, thinks this reminder of inferiority will constantly grind away at Reed. Reed, for his part, doesn't give a crap, and is simply happy that his daughter is alive.
Doom gets hit with this again in Grant Morrison's mini-series "1-2-3-4", when he attempts to use an alien computer called the Prime Mover to play a four-dimensional chess game against Reed, thinking he can destroy the team's familial bonds. The key to Reed's outplaying Doom lies in that family connection:
"My family are an equation. Alter one part of the equation and it no longer tells the truth. You failed from the start. You can no more change our essential nature than you can change E=MC2."
Numerous times, Magneto openly asks the X-Men why they waste their time fighting for a world that hates and fears them so much, assuming they make natural allies. When he eventually joins the team, Magneto realized how much of his past hate and experience has warped him.
In an Avengers/X-Men crossover, Magneto develops a helmet to alter human minds, thinking it's a great way to unite the world. Captain America tells him this is wrong and Magneto uses the helmet to remove any anti-mutant feeling from Cap's mind, assuming this will sway him. When Cap says he still feels the same, a stunned Magneto confesses he always assumed every human had a hate of mutants in them. The realization that Cap truly feels this way rocks him enough to destroy the helmet and surrender himself.
It's clear many of the anti-mutant bigots who push the idea of "mutants want to destroy us" are unable to accept that A) not all mutants are alike and B) that people with power would want to live a normal life and not use that power to oppress others, because they themselves would abuse their powers if they had any.
Stryfe sets up a trap for Cyclops and Jean Grey where they find a child (really a robot) tied to a computer system and tells them that killing the child will kill Stryfe. At the time Stryfe believed he was the child Cyclops once abandoned and thus totally believes they'll do it. He's literally shocked speechless when instead the duo fight the massive number of robots Stryfe sends after him and the caption boxes note how his entire worldview is being shattered.
During the Amazing Spider-Man tie-in to Secret Empire, Doctor Octopus attempts to reclaim Parker Industries from Peter, only to watch in horror as Peter destroys his company to keep it out of his hands. Doc Ock yells out asking why someone could be so unbelievably petty to do such a thing, but Peter tosses it right back, telling him that a man would willingly lose everything to protect people.
The criminals targeted by The Punisher are forever yelling at him that killing them won't bring his family back or impact crime in any way. It never occurs to them that Frank is perfectly aware of this and that he has simply devoted his life to killing scum until he dies.
In "Six Hours to Kill", he's poisoned by Baltimore criminals who want to use him as their own attack dog. He kills the guy who injected him and spends the next few hours killing criminals as usual (and because Baltimore isn't his usual turf, quickly goes through those on his list)... and is actually disappointed when one of his captors injects him with the antidote with seconds to spare.
One would-be baddie tries to rattle the Punisher by sending out people surgically altered to look like the Punisher's past victims. He believes this will shake up Frank and that he's constantly haunted by the nightmares of faces he's killed. When he confronts the man, Frank points out the key problem with this entire plan:
Punisher: What makes you think I'm haunted? I send them to hell. I sleep just fine.
The Mighty Thor: While living in Midgard against his father Odin's wishes, Thor falls in love with a mortal woman named Erika. Loki convinces Odin to let him continue with his romance, until Thor is called away to intervene in a war between realms. When he returns, he finds that he has been away a lot longer than he realised, and Erika has passed away from old age waiting for him. Loki is certain that this heartbreak will be enough to drive Thor to return home to Asgard. However, to Loki's astonishment and Odin's infuriation, the experience has only deepened Thor's love for Midgard, and he stays there to celebrate Erika's memory.
Loki: Why, brother? Loving them will only ever bring you pain and suffering. More than even I ever could. It's almost as if... Heh. Loki isn't your greatest enemy after all. And never will be. No... it's Midgard.
In Archie Comics' Sonic the Hedgehog, Dr. Finitevus turned Knuckles into an insane and ultrapowerful villain and, as a security feature, made sure that the change couldn't be reversed without someone dying for it. That should do it, right? When he explained this, there was silence... for about a second, at which point everyone present started volunteering. Then the next time Finitevus ran into Knuckles, he honestly seemed surprised when Knuckles refused his offer of alliance; it didn't seem to occur to the "good" doctor that Knuckles would hold a grudge over the brainwashing and the death of his father (who performed the above mentioned Heroic Sacrifice).
For that matter, The Plutonian himself doesn't actually understand good and never did. The reason he was The Cape for so long was because of a deep pathological need for mindless adoration brought on by his shitty childhood. He was never actually interested in justice or being good, he just mimicked these actions to get the approval he craved.
In volume 2 of Empowered, Emp saves a thug's life by warning him about his impending brain aneurysm and getting him to the hospital in time for an operation. However, on her way out, a pair of nurses drag her into a closet and drug her, complaining that she's ruined the evil scheme they're running from the hospital. The two of them are convinced that Emp's presence means the Superhomies are onto them, since there's no way a superhero would care about the life of a common thug. However, in this case, it's less because they can't understand kindness, and more because most superheroes in this series are assholes.
In Star Wars: Legacy, Darth Krayt's attempts to convert Cade Skywalker into a Sith fail because Cade doesn't want the power Krayt is offering him. Keep in mind that at this point Cade is still rejecting the Jedi calling—he just doesn't want power, light or dark. The idea that someone might not want power is something utterly alien to the Sith, who all more or less became Sith because they wanted power.
DuckTales: In the "Scrooge's Quest" arc, Scrooge exploits this to get the upper hand on Glomgold again after his enemy has managed to take over the city in his absence. He wanders around, doing everyday activities and periodically noting that a particular time has come around again. Glomgold goes crazy trying to figure out what sabotage Scrooge is perpetrating, and Scrooge is able to work this into getting everything back the way it was. Explaining to the triplets, he says that Flintheart drove himself crazy thinking of all the things he'd do to Scrooge if their positions were switched.
The Evronians from Paperinik New Adventures have a similar characteristic: in spite of being Emotion Eaters, the vast majority of them don't actually understand the power of emotions outside of food for themselves, nor have a large emotional ability to feel them. This proves to be the undoing of more than a few of them, who either don't anticipate someone else's reaction to their otherwise good plans or lack the emotional self-control necessary for some thing... And makes the few who can that more dangerous, as they come as a genuine surprise. Or, in one even more surprising case, a genuinely good person.
In Bitch Planet, overweight and sardonic Penelope is being "tested" by the ruthless prison wardens by being forced to look into a mirror that shows her what her true ideal self is. The wardens believe this will "help" Penelope by showing her as what they think is the ideal woman (thin, beautiful and sedate). Resistant at first, Penelope looks into the mirror...and it's her own reflection. The wardens are baffled, convinced the device must be malfunctioning, unable to understand why an overweight and unattractive woman would be happy with that appearance.
Lucky Luke: The Bounty Hunter: The title character cannot comprehend why Luke prioritizes justice over money.
The Simpsons: In one issue, Lisa tries selling seeds, only to be told by Mr. Burns to stop since he's an Enemy to All Living Things. When Springfield gathers together to have a seed fair anyway, Burns is confused. Smithers suggests that maybe the people of Springfield have learned to work together to overcome a mutual obstacle. Burns considers this for a moment, then decides they're just being impudent.
Valhalla: Although an Unsympathetic Comedy Protagonist rather than an outright villain, Loki, being the god of lies, deceit and politicians, is a fundamentally dishonest person and can't really grasp the concept of being honest and truthful. To him, everyone lies all the time and cloak their real agendas in pretty words. Heimdall gets a rise out of him in "Freya's Necklace" when he asks him what he could possibly know about honesty.