One possible reason could be that he might feel abandoned. Growing up without them, he could resent the fact that they left him an orphan. He might think that if they were really so great, they would have found a way to survive and be there for him.
He might openly oppose their policies. For example, if the Ministry tries to pass a law that restricts the use of certain spells for self - defense, Harry could publicly speak out against it, giving interviews or writing articles in wizarding newspapers.
Some writers might want to explore a different side of Naruto. Maybe they are tired of the same old positive - friendship - based stories and want to create a more edgy or dark take. They could be exploring what would happen if Naruto had a falling out with his friends due to some external factor like a power struggle or a betrayal that he wrongly perceives.
Well, this kind of fanfiction might be an interesting take on the character. It could explore a darker side of Harry Potter that we don't often see in the original series. Maybe the author wants to show how all the pressure and trauma he has endured could lead to a more cynical view of those around him.
One possible reason could be the way the Dursleys treated him. They were cruel, made him live in a cupboard, and constantly belittled him. This kind of mistreatment over the years could easily lead to hatred. Another aspect could be the lack of connection to his wizarding family that he was not aware of for a long time. He might feel angry at his parents for leaving him in such a situation without any real protection from the Dursleys.
It completely flips the usual narrative. In the original story, Harry has a sense of longing for his family, especially his parents. But in this fanfiction, the hatred changes the emotional core. It makes Harry a more complex and perhaps darker character. The relationships that were once sources of strength, like his connection to his parents through their sacrifices, now become sources of bitterness.
In the original series, Harry is an only child, so the very concept of a sister is a huge deviation. This changes the family dynamics completely. Instead of just having the Dursleys as his only family situation outside of Hogwarts, now there is this sister factor.
One consequence could be a breakdown in their friendship. His friends might feel hurt and start to distance themselves from Harry. For example, Hermione, who is very loyal, might be deeply offended if Harry constantly doubts her.
In some fanfiction, the author might create a plot where Harry has been betrayed before. So, he has trust issues even with his friends. For example, if he was tricked by someone who seemed like a friend in the past, it could make him more cautious and less trusting in new situations with his real friends.