Perhaps it's a miscommunication issue. Snape has a very complex personality. He doesn't show his emotions easily. Harry, on the other hand, might misinterpret Snape's actions and Snape might misinterpret Harry's intentions as well. This cycle of misunderstanding could fuel Snape's hatred in the fanfiction. Snape also has his own dark past and secrets, and Harry's presence might constantly remind him of things he wants to forget, like his unrequited love for Lily, Harry's mother.
One possible reason could be his lingering resentment towards James Potter, Harry's father. Snape and James had a long - standing feud during their school days. Since Harry looks a lot like James, Snape might be transferring his old grudges onto Harry.
One possible reason could be that fanfiction often takes creative liberties that may distort the complex character of Snape that J.K. Rowling created. Snape has a very intricate backstory and personality in the original series, and fanfiction might simplify or misinterpret it.
One possible reason could be Snape's past experiences. Maybe he had a difficult childhood himself and doesn't know how to handle having a son. He might project his own insecurities and traumas onto Harry. Another reason could be that he sees too much of Harry's father in him. Since Snape had a long - standing feud with Harry's father, seeing those traits in Harry could trigger his hatred.
Well, the Dursleys were extremely cruel to Harry. They locked him in his cupboard under the stairs for a long time. They also tried to prevent him from knowing about his magical heritage, which was a big part of who he was. Harry must have felt a great deal of resentment towards them for suppressing his true self.
One possible reason could be that in the fanfiction, the author might explore Snape's complex past with Harry's mother, Lily. Snape's love for Lily could translate into a more nuanced view of Harry. He may see parts of Lily in Harry and that softens his hatred.
One common reason is Snape's lingering hatred for James Potter. Since Harry looks so much like his father, Snape might take out his old grudges on Harry. He sees James in Harry and can't help but be reminded of the past bullying and his unrequited love for Lily. So, he acts hurtfully towards Harry as a way to get back at James, even if it's not really fair to Harry.
One possible reason could be Snape's long - standing grudge against James Potter, Harry's father. Since Snape had a difficult past with James, he might project that onto Harry. Another reason could be that Snape is trying to protect Harry in a very strange way. He may think that by rejecting Harry, he is keeping him at a distance from the dangerous wizarding world politics and plots that Snape is often involved in.
One possible reason could be that in the fanfic, Snape realizes Harry has more of Lily in him than he initially thought. Harry might show kindness or a particular trait that reminds Snape of Lily, softening his feelings.
One reason could be a conflict of interests. If they are competing for the same thing, like a magical artifact or a position in a magical society, and Susan uses underhanded tactics, Harry would hate her.
Another possibility is that there is some sort of personal misunderstanding between them. Maybe Susan Bones accidentally reveals one of Harry's secrets or makes a wrong assumption about him in public, which embarrasses Harry and leads to his hatred. Also, it could be that her family background or family connections play a role. If her family has some past issues with Harry's family or friends, it might fuel Harry's negative feelings towards her.
One possible reason could be that Snape shows a different side to Harry in the fanfiction. Maybe he protects Harry secretly from some hidden threats that others are unaware of, which makes Harry start to trust him.