"Look at these people; amazing how sheep'll turn up for the slaughter No-one condemning, they're lined up like lemmings and led to the water Why can't they see what I see? Why can't they hear the lies? Maybe the fee's too pricey for them to realize..."
In Death Note, there are interviews of the "man on the street" indicating widespread public support of the Knight Templar protagonists and their extreme "tough on crime attitude". This is in spite of the fact that in both cases the templars in question suggest that they plan on broadening their list of targets once they get rid of the truly evil people.
Saint Seiya: This was used as a humanizing move in the Hades arc. It's revealed that the Spectres in Hades' believe he is trying to bring about a Utopia Justifies the Means for all humanity... the "Great Eclipse" being the means. Of course, Hades just has a vague and nebulous all consuming contempt towards humanity and the living, and wants all existence to be in an orderly dead state.
One Piece: Nico Robin's tragic back-story had her betrayed left and right by the people who sheltered her so that they could collect the bounty on her head and hand her to the World Government.
To Aru Majutsu no Index: Stiyl and Kanzaki wipe their friend Index's memory yearly because the church told them she would die otherwise. The church was right, but only because they had put the curse on her themselves.
The citizens of Latveria are usually portrayed as genuinely fond of Doctor Doom, and willing to stand up for him against the likes of Captain America or the Fantastic Four. With good reason, he's responsible for freeing them from an unpopular dictator and subverting Reed Richards Is Useless by making Latveria one of the most prosperous countries in... Europe? All he asks for is the unconditional loyalty of his citizens. Some citizens are aware they will be killed horribly if they screw around, Depending on the Writer.
Following Marvel's Civil War, most of the US population is perfectly willing to acclaim psychotic murderers like Norman Osborn and Mac Gargan (a/k/a the Scorpion) as heroes. Despite the fact Norman has been found guilty of being the Green Goblin, and consequently is a known lunatic and mass murderer. They proved equally willing to demonize well-known heroes like Captain America and Spider-Man pretty much on command.
Despite all his boasting and legitimate prowess, Darkseid has been defeated, publicly, several times. Each time, the people of his world that he has brutally oppressed for untold generations help him back up, metaphorically or literally, instead of booting him out or just leaving him to die. Partly because they fear his retribution if he recuperates on his own and they don't help, but mostly because, thanks to the mindset he instills in every one of his "subjects", well...
I am many things, Kal El, but here, I am god
There's also the fact that Darkseid has lieutenants like Granny Goodness, Desaad, Kalibak and the like. As long as they're not publically abandoning him, attemping to boot him out or leave him to die is probably a bad idea ... and most of them will stick by him through rough patches either because they actually do think he's a good leader or because they realize just how bad their lives could get if one of the OTHERS took over. Desaad has turned on Darkseid in the past on occasion, when he thought Darkseid was truly beaten and he could take over. It never ends well for him. He's fortunate that Darkseid considers the attempts pathetic enough to be amusing.
Films — Animation
Madagascar: Melman the Giraffe is one, especially in the sequel.
In the novel The Hunchback of Notre Dame: Quasimodo, our "hero," believes that Frollo's guards are the good guys and the gypsies are the bad guys. The actual situation is that Frollo's guards are trying to kill Esmeralda (the woman Quasi is trying to protect) while the gypsies are trying to save her. So you have Quasi systematically thwarting the efforts of the gypsies while making every attempt to help the guards.
Trollslayer has Gotrek and Felix encounter a village that helps an evil sorcerer who is holding their children hostage. The heroes don't find out that he's mutated them all into his personal army until after they've killed them all.
Wicked: The citizens of Oz are like this, eating up everything the Wizard and Morrible say about Animals, and later about Elphaba. After trying to fight the propaganda and failing, Elphie turns this to her advantage when the rumor that "her soul is so unclean/pure water can melt her!" is put to the test.
In The Legend of Zelda: A Link to the Past, a number of villagers believe Link to be a criminal who has kidnapped the Princess due to propaganda disseminated by Agahnim, who has deposed the king. Two will even call the guards to attack Link if she sees him.
In Pokémon Diamond and Pearl, the grunts from Team Galactic fit this description. They believe Galactic is a natural energy company, and only battle the protagonist because they were promised rare Pokemon in return. Little did they know they're evil leader's main ambition was to destroy this world and create a new universe he could rule. Brilliant, guys.
The people of Unova are consciencious of their Pokemon to a fault. At Accumula Town, Ghetsis Harmonia makes a speech about the virtues of Pokemon liberation and how Pokemon can never truly be equal to humans while bound to a ball - and they just eat it up. It's only after Team Plasma gets a little too overt that the League starts taking action when all someone had to do to potentially derail the entire plot was present a historical overview of Pokemon crime history in theotherfourregions as a counterpoint back at Accumula. Oh, and for someone to give N some much-needed TLC; that'd be great, too.
Wizard101 most likely has few instances, however the most glaringly obvious example from the game is Crab Alley
Used in The Spoony Experiment during his review of Final Fantasy VIII. Doctor Insanonote making his first appearance is elected President of the US, and his inaugural address consists of him berating the American populace for being so stupid that they elected a man who didn't even bother hiding the fact that he's a thoroughly evil Mad Scientist. This is of course a gigantic parody and lampshading of a plot twist in the game, where the Sorceress (who is Obviously Evil) is made leader of a nation and the people cheer for her even as she openly insults them.
"My election platform was to build a giant robot sawblade that would cut Canada off at the top and then attach it to Australia so they wouldn't bother us anymore! My vice president... is Fu Manchu! What the hell is wrong with you people?! I'm pretty sure that's not even legal! Oh, man, we are so going to jack this country up beyond repair!"
Futurama The XXXI century people elected as president... the head of Richard Nixon. Do I need to say anything else?
Avatar: The Last Airbender: The citizens of the Fire Nation are portrayed as pretty much exactly the same as the citizens of the Earth Kingdom, with the main difference that they're completely dedicated to The Empire after swallowing about a hundred years worth of propaganda and having information about various acts of war kept from them. While this could be attributed to any group of citizens during the rule of a power others would call tyrannical, this really gets shown for what it is when the new Fire Lord, Zuko, takes power and instantly ends the war, at which point every Fire Nation citizen shown is completely behind him. Looks like they might just love their rulers too much.
Superman: The Animated Series: Used to an expert degree in the series finale. Superman finally knocks over Darkseid, tells the citizens of Apokolips that they're free... and to his dismay, they help the fallen despot to his feet and take him off to recuperate. "I am many things, Kal-El... but here, I am God."
This example borders on straight up Religion of Evil. The people of Apokolips are pretty much brainwashed slaves that worship their cruel and tyrannical God for being cruel and tyrannical.
Strongly implied to be this in the Justice Lord's universe before they changed things in the Justice League episode "A Better World", where Lex Luthor was President of the United States, in spite of his history of villainy, and had apparently killed the Flash. Superman killed him in the end, but this tendency convinced him and the rest of the then-League to become tyrannical overlords.