Short version: Being older and wiser doesn't make you evil.
If you read Harry Potter fanfiction, you've seen this before. There's a character in a position of authority. They are incredibly powerful, but for various reasons cannot directly apply this power. Instead, they act through the main characters, to whom they offer advice and assistance as they can. Typically, they are extremely old.
And fanfiction writers hate them like rats.
For some reason, something about this character archetype brings out the worst in fanfiction writers. Inevitably, every act they take to assist the heroes gets turned in fanon into acts of manipulation. Every bit of advice they give is turned into layers of half-truths and doublespeak. Every move they make and article of clothing they don become tools of control.
Usually they're painted as being the real villains of the tale.
As I mentioned, this is a major problem in the Harry Potter fandom. Dumbledore has taken massive amounts of hatred over the years, dating back to a surprising distance in the canon. It appears to be almost an unofficial standard of fanon that he was a manipulative exploiter who shaped Harry into a weapon to kill Voldemort, with no regard towards his feelings on the matter.
(If you want the ultimate in it, look to the
zelda_queen sporking of "Time To Fix The Mistakes", where insane!Harry considers killing Voldemort secondary to destroying Dumbledore's career when it comes to ensuring the present day will be safe.)
The My Little Pony: Friendship is Magic fandom has similar issues when it comes to Princess Celestia. It's rare to see anyone who portrays her in a positive light. The majority of fanfics portray her as a power-hungry bitch who deliberately arranged for her sister's possession to have an excuse to exile her to the moon. At least one claims the mantle she wears is a tool that forces people to respect her.
The list goes on. Almost the only advisor who doesn't get some form of dismantling by the fanbase is Master Splinter.
And the worst part is that there's next to no canonical basis for any of this.
I'm not a fan of Dumbledore. I consider the way J.K. Rowling treated his sexuality to be horrid, and find the character himself to be bland and too much of an expository tool. But the man is not nearly as bad as written. Even if he were manipulating Harry (and the fans are reaching for evidence sometimes), he has every reason in the world to do so - Voldemort cannot be allowed to run rampant, and the last time Dumbledore directly applied his power, his family was torn apart.
Princess Celestia I will defend much more strongly. The idea that she would have done anything to deliberately dispose of her sister is laughable - or else she wouldn't have shown so much happiness at seeing Luna restored at the end of the pilot. The idea of her as a power-hungry manipulator is even more hilarious, given how uncomfortable we see her every time she's in a formal situation. (The way most fanfic authors write her, she would be soaking it up at the Grand Galloping Gala; in canon, she invited her student and her friends because she could count on them to bring it to an abrupt halt.) Most fanfic authors who demonize Celestia appear to do so only because they don't have enough creativity to create an original villain.
This appears to be a major motivator for many of the demonizations, come to think of it. If you look closely at many demonizing portrayals of advisory characters, the authors have merely taken the villain's character traits and applied them to the advisor. It's a cheap way to create a villain without having to stretch the mind too hard.
Another possibility is out of dislike for any character with that much power who doesn't directly step in and settle the situation with flashy powers/laserbeams out the vagina/exploding flatuence. This is a major reason insane!Harry hates Dumbledore in "Time To Fix The Mistakes", even though power couldn't possibly have settled the situation. And indeed, in the majority of cases, it can't, and the authors seem unhappy with it.
And then there's the simple answer: the author's writing a Mary Sue fic and doesn't like the idea of anyone being smarter than their characters without cheating. Step forward, Rose Potter and your "Dumbledore's eyes twinkle because he's committing mind rape".
You have so many other characters to hate, fanfic authors. Leave the Dumbledores and Celestias alone.