It's definitely true sometimes. The tortured revolutionary that took it too far is a very common trope. A lot of the time, it's just very wishy-washy, as you'd expect from a mass produced cash machine like Marvel. When you're making so many stories, they're not all going to be winners, for any number of reasons. The people that think Marvel is making propaganda are just looking for it. The movies just aren't that good, they're not hiding some sinister motive
Have you watched a superhero movie or read a comic book? Nearly every villain is just a violent person trying to change things and the hero fights to keep things the way they are.
That's actually a common trope. It may or may not be conscious from the writer.
If you WANT a character's radical ideas to seem evil (because you believe it is evil), you make that character kill puppies. There are various examples like the boss lady in The Devil Wears Prada, or Cruella, or Poison Ivy,, or Magneto who are clearly evil because they do clearly evil thing, but they have a line here or a point there that actually makes a lot of sense, but since the character is obviously evil because of all the other puppy-kicking they do, that radical idea is of course evil too.
And sometimes, someone makes a YouTube analysis on why Magneto or Poison Ivy are actually kinda right in their social message - but that's crazy talk, because who would side with Magneto when he wants mutant supremacy? With Poison Ivy who wants to kill all humans?
Batman (the comics, anyways) is full of villains like that. Mr. Freeze just wanted to save his wife and went off the deep end after people pulled the plug on her cryogenic stasis pod, killing her. Poison Ivy was a biologist who worked on saving the world from ecological collapse and came to the conclusion that humanity would never change in time to save itself, so the only way to save the world is through violence, which is why she usually targets companies polluting the environment and their owners. Cat Woman is often depicted as either a petty thief making big scores for the thrill of it, or Robin Hood, stealing from the rich and donating the money to cat shelters and stuff. Sure, there are plenty of more standard villains in Batman, but when done right, Batman is largely the story of a broken man trying to save other broken people and stop them from hurting themselves and others.
The most literal example of a villain trying to save the world I can think of is Ozynmandias in The Watchmen. The story revolves around a plot by Ozymandias to basically explode two nuclear bombs and make it seem like attacks by Dr Manhattan in order to stop the Cold War from going hot by uniting the Soviets and the US against him. The comic is a total deconstruction of the genre, but it's definitely the most outright "the villain saves the world through mass murder" story you can find.