All Fall Down has Siphon suffer from this when she is arrested on the news, for the deaths and injuries her accidental power-stealing caused.
Atomic Robo: Robo's creator, Nikola Tesla, deliberately thrust him into the spotlight as an international celebrity as a protective measure; if anything happened to him, or if anyone tried to weaponize Tesla's technology, people would notice. Turning public opinion against Robo (through a False Flag Operation involving a stolen nuclear warhead) is how Majestic 12 finally gains the upper hand on him, allowing them to shut down Tesladyne and absorb its resources (and other Super Science institutions around the world) into the paramilitary Task Force ULTRA. Opinion swings back towards Robo's favor after he saves the world from a Biomega invasion.
The Green Hornet actually invokes this. Since his day job consists of him being the owner and publisher of a major newspaper, Britt Reed, he constantly has his newspaper run stories about the Green Hornet being a dangerous criminal mastermind so he (as the Green Hornet) can infiltrate criminal gangs who assume he wants a cut of their operation.
Katie the Catsitter has the Mousetress, who has been slandered as a villain despite being a superhero. Katie wants to help her get a positive reputation.
In Les Légendaires, the Legendaries, who used to be loved by the people of their fictive world Alysia, became Heroes with Bad publicity after their "final" fight with their Big Bad Darkhell by accidentally breaking a magic stone, causing it to accidentally trap everyone on the planet in the form of a child. The population ends up blaming them for this, and while they gradually get their reputation back, it's only after they saved the world from an Omnicidal ManiacGod of Evil that the population seem to have fully forgiven them.
This sometimes cause the population of Alysia to be portrayed as horribly ungrateful, seeing how they were quick to forget all the time the Legendaries risked their life (and keep doing so) for them just because of one accident that wasn't even lethal to the population.
Hartigan was framed for Junior Roarke's murder due to being one of the only clean cops on the force.
Marv already had a reputation of being a psychopath but going up against the Roarkes ensured that his name would be mud before execution. In fact, they initially ran afoul of him when they tried to frame him for murder.
Dwight is wanted for the murder of an established socialite; unlike the other two examples, he actually did it, although he was manipulated into doing so. His reputation was bad enough that he underwent plastic surgery to avoid being recognized.
In Sonic the Hedgehog (Archie Comics), following her brainwashing by the Iron Queen, NICOLE becomes a subject of fear to much of New Mobotropolis, particularly Idol Singer Mina Mongoose, who begins a series of musical protests against her. And things are made even worse when Ixis Naugus starts using Mina's music as a conduit for his magic, amplifying the public's distrust of NICOLE into paranoia and hate, in a bid to make himself a Villain with Good Publicity by promising to dispose of NICOLE for them. And it works, leading to a Heroic BSoD on NICOLE's part and a My God, What Have I Done? on Mina's part.
Richard Wentworth, The Spider, had a habit of killing crooks by the score. While this behavior was justified within the stories, it did make the police and public think of him as a dangerous criminal in his own right.
While this tends to come up at some point in most incarnations of Transformers, it was a particularly strong theme in the original Marvel Comics run, where the humans frequently weren't even aware that there were two factions of Transformers, let alone that one of those factions might be better-intentioned than the other.
In particular, Walter Barnett of the Intelligence and Information Institute, inspired by one of his son's comic books, hired its writer, Donny Finkleberg, to portray "Robot Master", who claimed to be in control of all the robots. When Finkleberg ended up a prisoner of the Decepticons, Megatron decided to keep the charade going, if only because it would invoke this trope for the Autobots. It didn't quite work, though, seeing as how it was kind of hard to explain why a madman bent on Taking Over The World would have two groups of robots under his control fighting each other, but fortunately for Finkleberg, he was able to escape before he outlived his usefulness to Megatron.
In the IDW sequel series Regeneration One, the Autobots definitely fall under this on Earth, seeing as how they failed to clean up after themselves when they left for good in 1991, and inadvertently let Megatron nuke the population to near extinction.
The Transformers: Autocracy and its sequel The Transformers: Monstrosity play with this. In the first, the Autobots are considerably hated by the populace, as they are a security force for the corrupt government, and their leader, Zeta, levels a city to stop the Decepticons, who are the oppressed masses forming behind a charismatic leader, Megatron, and numerous citizens sympathize with them. The Protagonists even team up with him to stop their corrupt leader, and the second Megatron blows Zeta's head apart, he turns on the Autobots and the rest of the populace. The Autobots managed to rally the citizens (as well as getting the press on their side), and oust the Decepticons. The sequel continues to play with it, as much of the populace doesn't trust the Autobots, partly because of the old government, but mostly because people don't want to get involved in a war. Dai Atlas uses this distrust to rally people against Prime, but even then a few civilians just consider Atlas's group a bunch of cultists. At the end, the Decepticons have been thoroughly discredited, and despite the good publicity, most Cybertronians just leave rather than join the Autobots.
The Transformers: Robots in Disguise has this once again toward the Autobots from the people of Earth, for very justified reasons. Humanity is aware that there are two factions of Cybertronians. They're also aware that in the instances where those factions have clashed, it's resulted in hundreds of thousands of human casualties and nearly got New York nuked. They're aware that Megatron is the leader of the faction called the Decepticons and is considered an enemy of the Autobots. They're aware that Megatron and Devastator were allowed to join them instead of being executed for their crimes. So humanity sees no reason to trust anyone who would turn around and let such mass-murdering war criminals join them with no apparent repercussions.
The Leopard from Lime Street, better known as Leopardman by the public, was feared by the people of Selbridge and hunted by the police due to being seen as either a criminal or a leopard monster. Given that he's a Spider-Man Send-Up, it makes sense that he's this, though since he's also The Cowl he often uses the public's perception to his advantage.
