Honestly, there could be multiple reasons. Maybe it was to protect Harry in the long run or to prevent a greater evil from emerging. It's a mystery that might be revealed as the story unfolds.
One reason is that fans like to explore different perspectives. In the original books, Dumbledore is presented as a wise and mostly benevolent figure. But some fans want to see what would happen if he had a darker side. It adds a new layer of complexity to the story.
Well, in some fanfictions, Dumbledore might want to punish Hermione if she goes against the school rules in a way that he thinks is particularly serious. For example, if she delves too deep into dangerous magic without proper authorization.
Perhaps James Potter, as Harry's father, wanted his son's story to be told in a more 'authentic' way. He might have felt that fanfiction could distort or misinterpret the real events and relationships in Harry's life.
Some fanfictions portray Dumbledore negatively because he made many controversial decisions in the original series. For example, his handling of Harry Potter's situation was sometimes seen as using Harry as a pawn in the fight against Voldemort. He kept many secrets from Harry that could have potentially changed the course of events and put Harry in more danger. Also, his relationship with Grindelwald in his youth and the events surrounding it add to the reasons why some writers in fanfics might choose to show him in a negative light.
Dumbledore might underestimate it because he's used to the 'official' version of the wizarding world. Fanfiction can be full of wild ideas that don't fit his traditional view.
In some fanfictions, Dumbledore might bow out of respect for a powerful magical entity or a person with extraordinary abilities. It could also be a sign of his humility in the face of a situation where he realizes he is not the most knowledgeable or powerful.
Yes, there are likely fanfictions out there with this dark and alternative take. Fanfiction often explores non - canonical ideas, and this would be a very radical one. It goes against the established lore in the official 'Harry Potter' series, but that's the nature of fanfiction - to play with different concepts.
In Harry Potter and the Deathly Hallows, Dumbledore, not Malfoy, was the real owner of the Elder Wand. However, when Dumbledore was injured by Dark Magic and needed a new wand, Malfoy tried to take the Elder Wand but was stopped by Dumbledore and his friends. Although Malfoy didn't really own it, he showed a sense of greed and jealousy when Dumbledore needed a new wand. He had tried to get the Elder Wand through deception and threats, and had succeeded. However, this also caused the relationship between the Elder Wand and Dumbledore to become even more tense. Dumbledore and his friends finally succeeded in destroying Malfoy's Elder Wand and protecting its true owner.
In some fanfictions, female Harry Potter might hate Dumbledore because the author wants to create a different dynamic. Maybe Dumbledore's actions in the original story, like keeping secrets from Harry, are exaggerated in the fanfic. For example, if he withheld information that could have saved someone she cared about, it could lead to her hatred.
In some fanfiction, Harry might not trust Dumbledore because the author wants to explore different power dynamics. Maybe they show Dumbledore keeping too many secrets, like about Harry's past or the true nature of the threats he faces. This secrecy can make Harry feel manipulated and thus lead to a lack of trust.