In fanfiction, the plot can deviate a great deal. Snape could be given a new role as a mentor figure. He might teach Harry advanced magic techniques in a gentle way, unlike in the original story. This new relationship dynamic would make Harry feel safe. Also, if Snape is shown to have a change of heart towards Harry's parents, especially his mother, Harry could feel a connection and thus safety with Snape.
One possibility is that the fanfic changes Snape's backstory to make him more sympathetic. Harry, being empathetic, then feels safe around him. For instance, if Snape's past is shown to be full of hardships that made him act the way he did, Harry might understand and feel safer in his presence.
In some fanfictions, it could be that the author has rewritten Snape's character in a more approachable way. Maybe Snape shows a side of himself that is protective towards Harry, like secretly guiding him in his magic studies without the usual harshness, which makes Harry feel safe.
One reason could be the re - imagining of Snape's character. In fanfiction, he might be kinder and more understanding towards Hermione than in the original story. So, she feels safe in his presence.
One possible reason could be that Snape has shown unexpected kindness to Hermione in the fanfiction. Maybe he has protected her from some danger secretly, which makes her feel she can rely on him and thus feel safe.
One reason could be that in this fanfiction, Snape has some hidden kindness towards Harry that he doesn't show in the original story. Maybe he secretly protects Harry from other threats, which makes Harry feel safe around him.
Often, it starts with a shared experience. For example, they might face a dangerous magical creature together. After that, Snape might show concern for Hermione's well - being, which begins to build her sense of safety around him.
Well, it could be that the fanfiction author has created a unique backstory. For example, Snape could have saved Hermione's life at some point in the past, and she now has this deep - seated sense of security around him. Also, he might be a source of knowledge for her, and his presence, while initially intimidating, becomes reassuring as she realizes he won't let harm come to her in matters related to magic and the school.
Perhaps it's because Snape is a complex character in the original story. Fanfictions might explore his character in ways that make Hermione seem protected in those fictional scenarios. For example, some fanfictions could depict Snape using his knowledge and power to shield Hermione from various threats within the magical world they inhabit.
On the other hand, Harry could be proud of himself for standing up for what he believes in. He may think that he has made Hogwarts a better place by getting rid of a teacher who was not treating students fairly. But at the same time, he might have mixed emotions as Snape was also an important part of the Hogwarts environment for so long.
Maybe if Snape had revealed his true loyalties earlier. Harry would then understand that Snape was on his side all along. This could lead to them getting along as they both fought against Voldemort. Snape's sacrifices for the wizarding world would make Harry respect him.
One possible motive could be a misunderstanding. Maybe Snape is framed for something really bad, like a dark magic plot against Hogwarts. Harry, in his haste to protect the school and his friends, believes Snape is guilty and takes drastic action. Another reason could be if Snape accidentally endangers someone Harry loves dearly, like Ginny or Ron, and Harry's emotions get the better of him in the heat of the moment.