Rurouni Kenshin, the flashbacks to the mid-1860s in the manga around the beginning of the Jinchuu arc and the Remembrance OVAs, and Ishida's group in Peacemaker Kurogane. However, in reality, the first wave of "Patriots of the Restoration" was a lot worse than shown in Ruro Ken, murdering any merchant who had dealings with westerners.
In Black Lagoon Rock encounters an ex-Japanese Red Army member in "Lock And Load Revolution". The old man was an idealist working for a world revolution, and verged into terrorism. After the movement fell, he joined forces with other terrorists, in present, an Islamic group led by a Lebanese Jihadist. Also, the super-Meido Roberta was a Cuban trained assassin and a FARC guerrilla who became disillusioned when she realized she was just a guard dog for The Cartel.
The Reverse Organization from Letter Bee have typically been displayed as not terribly nice people, but the government they've been rebelling against has shown hints of being equally not nice, particularly if half the things Reverse has said about them are true. However, they may have exceeded this trope and gone on to just straight 'evil' following recent chapters, wherein they used an innocent young nun as a human sacrifice, essentially destroying her soul and condemning her to a slow death in order to lure in a gigantic armor bug to attack the capital.
Magi - Labyrinth of Magic: In the Balbadd story arc, the anti-government Fog Troop were quite nasty before Alibaba took charge of them. So much so, in fact, that when Alibaba and Sinbad change the organization from thieves and vigilantes to a legitimate rebellion several members leave on the spot. Even worse, after the Fog Troop finally succeeds in overthrowing the corrupt king, all the former members of the Fog Troop show up... and use magic to work the citizens of the nation into a frenzy, turning the bloodless revolution into a massacre purely out of spite.
Metropolis: The Zone 1 rebels are shown to lash out against the defenseless robots, and launch a violent assault against the Marduks working for the Red Duke. Ultimately, they fail because their uprising was engineered by their opposition, and the rebel leader falls to a trap alongside his troops.
V for Vendetta: V makes no bones about the fact that he is a terrorist. note But he also recognizes that such a person (or monster) has no place building or living in the new world that will rise from the ashes of the old (the one he plans to burn down). He is an agent of death and destruction, a weapon to be cast away when it has served it's purpose.
Quite a few Star WarsExpanded Universe comics have attempted to extend this to the Rebel Alliance, trying to soften the line between good guys and bad guys, as well as explain how the cash-strapped outfit got its money. Sometimes its just down to the occasional jerkass pilot, such as Jal Te Gniev (who later makes a Heroic Sacrifice after watching a teenager he'd abused take the blaster bolt for him—and shooting with a gun that he'd bought to kill Gniev). However, it did sometimes come down to situations where in order to keep working, the Alliance and later New Republic would have to kill innocents themselves.
In fact, after the Rebels won at Endor, destroying the Death Star, one of the first acts of the New Republic they established was to execute Grand Admiral Osvald Teshik for war crimes after he was captured in this battle. With Palpatine and Vader dead, he was pretty much one of the highest ranking Imperials captured. Tragic fact that Teshik was one of the few decent Imperials.
Between 1980 and 1983, the Star Wars fandom was inundated with stories speculating on how — or if — Han Solo might be thawed out of the carbonite in which he'd ended The Empire Strikes Back. One particularly memorable story, "The Revenant", had him being unfrozen thirty years later. Leia is dead, Chewbacca is dead, Lando is dead ... and Luke, who arranged Leia's death to bring a group of unaligned planets to the Rebellion's side, is First Citizen of a New Republic oppressive as ever the Empire was.
The rebels in Proof of Life most certainly count. After they stopped receiving foreign monetary aid for the revolution, the guerillas turned into farming coca plants and kidnapping and ransoming important foreigners. They also have little qualms about shooting civilians or police officers.
The Wind That Shakes the Barley, starring Cillian Murphy, won the Palme d'Or award for its application of this trope to the Irish Revolution (and then the Civil War), so it must have done something right. note In Real Life, when the War of Independence ended, a significant amount of the next decade was spent by the new Irish government trying to get rid of the IRA, since they had been fighting for independence of the entire island, which the Free State government traded away, with the South becoming self-governing and then (with the Republic of Ireland in 1949) fully independent by itself. The Civil War (which is the worst things got) began when partition occurred under the Anglo-Irish Treaty, setting up the Free State government in the South. Much of the IRA became the Free State Army, while the rest rebelled, refusing to accept the referendum ratifying the treaty, seeking to unify all of Ireland.
The Alternate History film It Happened Here, set in a Nazi-occupied Britain, deliberately subverts the gallant resistance trope. The protagonist witnesses the death of her friends in a shootout between local partisans and German soldiers, and the movie ends with prisoners from a British SS unit being massacred by their captors.
Yuri: "I guess they [African militants] can't own up to what they usually are: a federation of worse oppressors than the last bunch of oppressors. Often, the most barbaric atrocities occur when both combatants proclaim themselves freedom-fighters."
The anti-government resistance group, the Fishes, quickly turn into this in Children of Men when the more radical Luke hijacks the organization, after assassinating his predecessor.
One of the most important tropes in the French film Army of Shadows. The film follows a cell of the French resistance battling the Nazi regime. While the Nazis are portrayed as terrible monsters, it's repeatedly highlighted that the French have to get their hands dirty as well. Much of their work consists of executing traitors, including their beloved female comrade. While the movie isn't a pro-Nazi film, it clearly suggests that war is disgusting and hellish even if you're one of the good guys.
Black Book catalogues Jews who were sold out to the Nazis by members of the Dutch Resistance. After the liberation, the Resistance harasses people who collaborated with the Nazis, even if it was done out of fear or as a part of their cover as double agents. To cover up their tracks, they even arrange a relatively good Nazi official to be executed for the crime of collaborating with the communist members of the Resistance.
In TRON: Legacy, Clu's revolution against Flynn's leadership kicks off with the genocide of the Isos, followed by establishing a police state that routinely "rectifies" delinquent programs into soldiers in Clu's army, or pits them in gladiatorial games to the death deresolution.
In The Baader Meinhof Complex, the Red Army Faction morphs into this trope over time. They start as a motley collection of political activists, juvenile delinquents, left-wing youths, and journalists who mainly participate in protests and rallies and undertake some occasional arson and vandalism with a political message. Eventually, they become brutal terrorists, robbing banks and bombing American military installations. Later "generations" of the group get progressively more radical and violent, taking and executing hostages, hijacking aircraft, bombing a newspaper, and assassinating and kidnapping public figures.
In contrast to the rebels of the later films, the Separatists in the Star Wars prequels are almost entirely shown as being evil. Their rebellion against the republic is little more than a big business backed attempt to rule the galaxy in the name of profit, with all of the big names fully aware of this. Being controlled by a sith lord and a homicidal cyborg certainly didn't help their causes reputation either. It's only the planets that revolt against the Republic in hope of receiving Confederacy assistance that actually believe in the moral cause beyond lip service.
Raza and his revolutionaries in The Professionals. Although the heroes have some sympathy for Raza's cause, we are still shown Raza's forces massacring the troops on the government train they capture.
In The Dark Knight Rises, Bane presents himself as a revolutionary trying to free Gotham from the control of it's corrupt elite. His methods? Gather an army mostly made up of mercenaries and escaped convicts, trap most of Gotham's police underground, put all members of high society and other dissidents through a Kangaroo Court, and threaten to detonate a nuke if anyone tries to interfere. And through all of this, Bane is not remotely interested in helping Gotham. The entire point of the "revolution" is to spread chaos and distract the populace from his true plan of destroying Gotham.
The Brotherhood in George Orwell's 1984, while having motives much more ethical than the Party's, are not much better in their methods. Made even more complicated by the fact that the Brotherhood may not even exist and everything O'Brien told Winston about it might have been a lie.
In the vein of the Militant Godless, Camus' The Rebel. Complete with atheist suicide bombers.
Fyodor Dostoevsky used this trope in his novel Demons. The revolutionists in this book are portrayed as ruthless terrorists, led by power-hungry Pyotr Verkhovensky, and their ideologist preaches about the necessity of wiping out millions of people for the victory of the revolution. At the end some of them are dead, the rest(except Verkhovensky) are arrested. What is even worse, the leader of this group has a prototype from real life - Sergey Nechaev, one of the most infamous Russian terrorists of that time.
In the third book of Dread Empire's Fall, guerrilla leader Sula leads a brutal resistance against the aliens, complete with car bombings, assassinations, and purposefully goading the government into executing innocent hostages. While she doesn't purposefully murder schoolchildren, she considers it their own fault if they wandered too close to her bombs. "Human warmth is not my specialization".
The theme of A Piece of Resistance, a novel by Clive Egleton set in a Soviet-occupied Britain. Innocent bystanders get killed and those at the sharp end find themselves manipulated, or even targeted for killing, by their superiors.
Ken MacLeod's Fall Revolution books jump back and forth in time quite a bit, but often imply that the various quasi-utopias in the far future were arrived at by, say, slaughtering a large percentage of the world's population.
This is a major theme in Mockingjay, the last book in The Hunger Games trilogy by Suzanne Collins. By the end the rebellion only avoids simply becoming a direct copy of the Evil Empire they were trying to replace by a narrow margin.
The Black Company, although POV is on The Empire side and revolution ultimately fails in the first book. Played more or less straight in the third book.
In On the Razor's Edge, Gidula tells Donovan that as Padaborn, his rebellion had killed many innocents who had just gone to their jobs early.
In Darkness at Noon, Rubashov ironically recalls having advocated civil war and other extreme measures as the only way to win the Revolution, and that as a Full-Circle Revolution its only consistency with past ideology is its denial of decency. Rubashov sees his nemesis Gletkin, who received none of his education in pre-revolutionary times, not as a betrayer of the Revolution but as its logical product, and calls him a "Neanderthal."
In Myst: the Book of D'ni, after Terahnee falls, the charismatic slave Ymur feels that only when the Ronay are slaughtered to the last child will there be any lasting freedom. He suffers Motive Decay quickly.
In The Powder Mage Trilogy it opens with the hero leading a coup against a corrupt king. The revolution quickly escalates to mass public beheadings of the nobility, riots, and war.
In Blood's Pride, Faroth and his revolutionaries don't pay much attention to nuance, and just want to kill all the Norlanders without regard to the fact that some of them are sympathetic (and also without regard to the fact that some innocent Shadari die too). Faroth also treats the revolution as if it were his personal property, and won't let anyone else have a leadership role. One character explicitly describes Faroth's group as more like a gang rather than the band of good people she'd hoped for.
The rebellion in Daughter of the Lioness. While the native Raka people have clearly suffered for centuries under terrible oppression, and the current monarchy is clearly corrupt, the rebellion has to do some very moral grey things to usurp them (including the murder of innocent children). The main character spends much of her time ensuring that it won't be more of a blood bath than it needs to.
A recurring element in the Takeshi Kovacs trilogy, where the ruling Protectorate is repressive and fascist but there's a lack of good alternatives. Kovacs is reluctant to join the neo-Quellist revolution in Woken Furies because in his experience, revolutionaries rarely turn out to be better than the people they're overthrowing. He had personal experience with this in Broken Angels with Joshua Kemp, a charismatic revolutionary who used Quellist rhetoric to justify using nuclear weapons on innocent civilians.
Alien Nation: Udara in the telemovie of the same name, a group of Tenctonese terrorists who resorted to brainwashing their own children into assassins and suicide bombers to fight the Overseers on the Slave Ship. Even after the slave's emancipation, Tenctonese sentiment was divided on whether the Udara were freedom fighters or extremists who did more harm than good.
Babylon 5: Has plenty of violent uprisings - Free Mars. Other Mars Resistance cells, the Narn Rebellion against the Centauri. The Telepath Resistance, however, straddle the line between this and The Revolution Will Not Be Villified.
Blake's 7: While La Résistance are clearly better than the Federation, the main cast are all anti-heroes at best and Blake is often called on his devotion to the Rebellion over taking care of his people. And then he was replaced with Avon, who didn't even pretend to take care.
"The Ark" has the Monoids, who were slaves for the humans until they rebelled.
In Warrior's Gate, the Tharils once ran a slaver empire, until the slaves revolted and enslaved them.
The rebels in "Day of the Daleks" are fighting the Daleks and are portrayed as quite brutal people, killing UNIT soldiers ruthlessly. A suicide bombing by them is responsible for a Stable Time Loop that caused the wars they were trying to prevent.
Revolution: Played with. Episode 3, episode 5, episode 9, and episode 13 show that some members of the resistance are very unmerciful to any Monroe militia member (former or otherwise), are willing to torture as part of interrogation, are willing to sacrifice civilians to kill off militia officers, and show signs of becoming similar to the militia. However, episode 14 and episode 16 show that some resistance members are careful to ensure that no faction uses an atomic bomb and anthrax as weapons in the war effort.
Star Trek: Deep Space Nine: The Bajoran Resistance. They were anti-heroes at the very best, had a running mantra of I Did What I Had to Do and were sometimes even explicitly referred to as "terrorists", and not just by Cardassians (though usually). Ditto the Maquis.
Kira Nerys: None of you belonged on Bajor. It wasn't your world! For fifty years you raped our planet, and you killed our people. You lived on our land and you took the food out of our mouths, and I don't care whether you held a phaser in your hand or you ironed shirts for a living. You were all guilty and you were all legitimate targets!
Unsere Mütter, unsere Väter: In this German drama, between the Germans, Soviets, and Polish Resistance, the latter are usually the best of a bad lot, but are not above a bit of pillage or anti-semitism. This is exemplified when they ambush a train bound for Auschwitz and loot it for weapons, but are prepared to leave the prisoners in the cattle cars to their fate.
V: The Miniseries: The Resistance used biological warfare against the enemy. Given that most Visitors lived in sealed starships and thus had the option of simply leaving unharmed, it's not quite as nasty as it sounds.
That Mitchell and Webb Sound played with this by having a pair of vapid TV talking heads discussing, in a very civilized manner, the boiling alive of Queen Elizabeth II after a clearly violent and horrible revolution.
Much of Tom Stoppard's The Coast of Utopia trilogy, set during the 19th century in Europe, primarily Russia and France. Let's just say it had a historical basis and one of its main characters was Mikhail Bakunin, and I don't mean the guy from LOST.
In the Crusader games, the Resistance is very, very much willing to use hardball tactics. The best example of this is the protagonist, the unleashing of whom on a target is not unlike using a tactical nuke, but in the manual it also notes that while General Maxis seems sincere in his ideals, the WEC has tried to get him to surrender himself, dismantle the Resistance, or do less drastically stupid things by threatening civilians. Maxis has never given in, nor tried a third option.
The Scoi'a'tel in The Witcher. The game does go to great lengths to explain the understandable grievances that led to their formation and continued existence (being conquered, treated as second-class citizens and subjected to violence and pogroms by the humans), but also makes it very clear that they are ruthless murderers who attack innocent or not-so-innocent civilians, sometimes in particularly gruesome ways, rather than the oppressing government's armed forces. Quite a few Dwarven and Elven NPCs express their profound dislike for them.
At one point early on, a member tries to convince Geralt to let him take some crates of medical supplies. If you give them to him, it later turns out they really contain some really nasty weapons that only work on unarmored civilians. Which they use to prominently assassinate an unarmed civilian. Who happens to have a second job as a drug pusher, making addicts of elvish teenagers so he can force them into drug-controlled slavery and/or prostitution. Or at least that's what the moderate dwarves and elves say. So, that one particular incident was probably justified, but later it gets worse.
The Defias Brotherhood in World of Warcraft may count as an example of this. The Defias began as a group of disgruntled stonemasons who were cheated by their government. Unfortunately, they became too heavily involved with criminal elements and ended up robbing and killing the peasants.
The Takers in Geneforge 2 (and to a lesser extent in Geneforge 1 as well). Then a fair chunk of the rebellion (especially the drakons) in Geneforge 3-5.
Rebels are always bad guys in the FreeSpace series, most notably the Neo-Terran Front, a violent anti-Vasudan rebel organization that believes it can forge an alliance with Omnicidal ManiacStarfish Aliens, and the Hammer of Light, a band of Scary Dogmatic Aliens who believe that the aforementioned Starfish Aliens are the prophesied "Great Destroyers" who must cleanse the universe to prepare it for the enlightened (i.e., the Hammer of Light themselves).
Both the UFLL and APR in Far Cry 2. Sure, they both claim to be fighting for their people's best interests, but really they're both as corrupt and vicious as each other. The game's ending has the player rejecting both factions and siding with The Jackal, and killing every named leader in either faction.
In Halo, there are secessionists who want to break off from the UNSC (they mostly appear in Expanded Universe material, outside of a few brief appearances in Halo Wars multiplayer and a few mentions in Halo: Reach and Halo 4). At the beginning of their campaign, they were viewed sympathetically, as all they wanted was their independence. This view largely ended when they began killing people (most infamously when one group deliberately nuked the Haven arcology, killing two million civilians and injuring 8.3 million), and now they're squarely in this trope.
The Renegades from Tales of Symphonia are a group dedicated to fighting the organization that "guides the world," Cruxis. How do they do this, you may ask? It's implied that most of the time, when a Chosen fails in the Journey of Regeneration, it's because the Renegades kill them, thus prolonging the cycles of Regeneration. Hell, even after forming an alliance, Yuan still resorts to his plan to hold Lloyd hostage and force Kratos to undo the seal. Even Kratos seems to acknowledge that Yuan is serious with his threats.
AVALANCHE in the Final Fantasy VII games are the protagonists, but certainly not civilized — Final Fantasy VII itself starts with these rampaging eco-terrorists committing a massive bombing, killing a lot of innocent people — and then the next day, they do it all over again! Not to mention the fact that some of the members (read: Barret) act thuggishly when not on the job too.
Played straight in Command And Conquer: Generals with the Global Liberation Army. Your first mission involves "liberating" a local village by flooding the valley it is in, wiping out half of the village in the process. Your second mission involves stealing aid supplies from more poor villagers, and you are explicitly ordered to shoot the villagers if they are taking supplies and level their homes. The third mission involves a massive riot and leveling and looting half a city, and by the final mission, you've gassed a major Chinese city.Any doubt that the GLA are not utter bastards is wiped away very, very quickly.
Armored Core is filled a bunch of extremely violent rebel movements who are either a) A fake movement or b) plans to start their rebellion by causing as much destruction.
Just Cause 2 has The Reapers led by Bolo Santosi and the Ular Boys led by Sri Iriwan. The path to "revolution" for both is to get Rico Rodriguez to, in Bolo's own words, turn Panau into a "smoldering ruin".
In Modern Warfare, Khaled al-Asad's revolution in his unnamed Middle-Eastern nation is explicitly shown to be brutal and violent, as the player experiences it from the perspective of the deposed President of the country as he's driven through the street. At first there's beatings and arrests in the streets, followed by civilians being shot as they run away and execution squads shooting people in the street. It ends with the President being marched into a square and executed on international television.
The revolution in Valkyria Chronicles II is essentially a racial purge led by racist nobles opposing the Archduchess for revealing her Darcsen (Fantasy Counterpart Culture equivalent of Jews) roots. Later on, it's revealed that it's really just a coup for Count Gassenarl to usurp the throne.
The mage revolt in Dragon Age II is very brutal, and when Thrask goes down the hotheads take control and run away with it.
In Freelancer, there are many factions triyng to overthrown the Colony government. Every Colony has at least one. In storyline, Lane Hackers, Blood Dragons and Bundshchuh are even played as good guys. And even other factions like Mollys actaully have at least not ultimately evil intentions. But how all this factions making their point? By attacking innocent trade convoys not unlike other utterly criminal pirate factions without any morale.
In Bioshock Infinite, the floating city of Columbia is controlled by Zachary Comstock and the Founders, xenophobic white-supremacists who brutally oppress all black, Irish, Chinese and Indian citizens within the city. Opposing them is the Vox Populi, made up largely of the people mistreated by the Founders and led by Daisy Fitzroy. The Vox Populi's grievances are understandable, but they have degenerated into vicious marauders who mercilessly bully and butcher the citizens of the city. When the revolt gets underway, Booker and Elizabeth come across the aftermath of many a firing squad and towards the end, Fitzroy even tries to kill Booker and Elizabeth (though Burial at Sea retcons this into her working with the Luteces by serving as a Stealth Mentor).
Vox Populi member: Your homes are ours! Your lives are ours! Your wives are ours! It all belongs to the Vox!
Booker DeWitt: When you get down to it, the only difference between Comstock and Fitzroy is how you spell their name.
The NSF note National Secessionist Force from Deus Ex. The game starts with JC going after them to retrieve a couple crates of plague cure they stole to give to the poor. Whether they should be considered terrorists or Well Intentioned Extremists is rather up for debate. All part and parcel of the game's Grey and Grey Morality.
In Syndicate (2012), the Syndicates are unquestionably evil by 20th/21st century Western standards. However, the Subverters opposing them are Bomb-Throwing Anarchists little better, who are unable to offer any alternatives other than "kill as many bourgeois as possible", with leader of the New York branch Kris Delaney gleefully anticipating the civilian collateral damage. It's hinted that a less militant wing of the Resistance is working on a more scientific solution, but you don't see them in the game.
The Elder Scrolls V: Skyrim has two of these: The Stormcloaks, a significant chunk of which is blatantly racist in their 'Skyrim for Nords' approach, and the Forsworn of the Reach. While the Forsworn definitely have good reasons to feel angry, the wholesale slaughter of civilians combined with a tradition of human sacrifice and alliances with thoroughly nasty monstrosities kind of ruins the 'noble rebel' effect. The Forsworn's leader acknowledges this, saying there are no innocents in war, only the guilty and the dead.
The Chots from Messiah were originally rebels against the dictatorial rulers of Earth, but with time have degenerated into a society of sewer-dwelling, savage cannibals. They don't even remember their origins anymore and don't fight for any cause (save for that of having enough people to eat.)
Homefront: The protagonists joins the Resistance who are willing to use white phosphorous mortars on GKR mooks, who are portrayed as monstrous. But the Resistance are quite tame compared to the survivalists who are jerks to everyone who aren't on their side, and are very racist against Asians.
The Pitt DLC for Fallout 3 has an overarching theme of Gray and Grey Morality, exemplified in the struggle between Ashur's brutal slave regime trying to engineer a cure for the mutations plaguing the place, and Wernher's rebellion who want to just as brutally take the cure by force. Also, the cure is a baby.
The various Jidahist factions in Shooting War, though Abu Addalah takes the cake.
Tech Infantry has various rebel factions, from the Christian Federation and their penchant for suicide-ramming freighters into enemy vessels, to the Liberation and their campaign of terror-bombings. Even the Resistance has as their main gripe the fact that supernaturally-powered humans are forced to serve in the Tech Infantry Space Marine forces. These forces are fighting against alien Bugs that want to eat everyone, other aliens that want to kill all humans and take their planets as living space, and still other aliens who want to enslave humans and work them all to death. This makes their occasionally violent tactics seem a bit extreme.
Although the Earth Federation and the Middle Kingdom that replaces it are both quite nasty, the aliens — especially the Bugs — are usually worse, and the endless rebellions, mutinies, and civil wars make it darn hard to fight the Bugs as a united front.
A World of Laughter, a World of Tears sees the nonviolent Civil Rights Movement collapse thanks to a drastic misreading of the political climate by President Disney. Martin Luther King, Jr. gets publicly egged, destroying his credibility, and the movement falls under control of the Nation of Islam. One word: jihad.
The French Revolution in Look to the West starts out being as violent as our history's...and never really calms down. In the long term this has the effect of forcing nearly all reformist movements to be more nonviolent by default, just to avoid the comparison.
Both this trope and it's inverse characterize the Red May Revolution in Reds While the communist revolution in America doesn't lead to a Soviet style nightmare, it is far from a tea party. The revolutionaries may have the moral high ground in the face of the dictatorial reaction by the old regime, but they still have their own Red Terror and Kangaroo Court system. Anti-authoritarian currents in American society appear to have won out by the present day, as the Red Terror seems to be pretty universally regarded as a mistake.
In the short story The Revolution, the protagonist witnesses his wife, oldest son, and scores of others die at the hands of his own government. Once given the chance to fight back, he racks up 134 kills in just a few months, and vows to not stop until the rest of the tyrannical government is dead or about to hang.
Jet's Freedom Fighters are not a particularly nice bunch. Despite being a charming group of kids who initially help out Team Avatar, they're actually willing to do pretty terrible things to wipe out the Fire Nation. At one point, they attempt to flood a town filled with innocent civilians, simply because the Fire Nation was occupying it. To their credit, the group realizes their mistake and makes a Heel-Face Turn shortly after the flooding fiasco. Despite efforts to do the same, Jet himself ends up stuck in the Heel-Face Revolving Door, though he eventually ends up on the right side.
The Omashu Resistance also does some unscrupulous things in their efforts to drive out the Fire Nation occupying their city. The first thing we see them do is attempt an assassination of the governor's family, including his infant son. Again, they perform a Heel-Face Turn shortly afterwards.
The main antagonists of The Legend of Korra are the Equalists, a revolutionary group dedicated to seizing more power for non-benders and attempting to bring down bending all together. After a terrorist attack in a public event, they end up bombing the city- and while the show can't explicitly say civilians died, anyone looking at the wreckage knows they did.
The Decepticons from Transformers are occasionally this, depending on the incarnation. In particular, Transformers Animated and the Alignedcontinuity depict the Decepticons as having legitimate grievances with a morally grey Autobot government, but they're just too extreme in their methods. Beast Wars suggests that the Predacons might be in the same boat, but we don't learn enough about the situation to properly judge.
In Transformers Prime, for instance, the Decepticons were originally a movement to abolish the Caste System that had large portions of the planet functionally enslaved. They then grew so brutal that their home planet was turned into a lifeless husk, and the Decepticons slowly came to care more about winning, or at least making their opponents lose more, than actually trying to make a better future.
Liberty's Kids takes a relatively balanced look at The American Revolution for its intended audience. For instance, while it treats the overall goals of the American Independence as a good thing, the negative elements like mob violence, slavery and the privations Native Americans suffered in the conflict are not overlooked while the British/Loyalist side are allowed to express their point of view.