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.
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 that he sees her intelligence and potential. Snape has always had a soft spot for those who are brilliant in potions and magic, and Hermione is top - notch in that regard. He might also recognize her determination and how she's often an outcast among her peers in a way, just like he was. So, he feels a sense of kinship and thus protectiveness towards her.
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.
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.
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.
Percy is very brave. He doesn't hesitate to jump into dangerous situations, and Annabeth knows that he'll protect her. So his courage makes her feel safe.
In some fanfictions, it could be because Draco shows a different side of himself. Maybe he protects Harry from other threats secretly. For example, he might use his knowledge of the Slytherin world to keep Harry out of danger.
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 fanfiction, Hermione might feel protected by Remus because he is a skilled wizard. He has experience dealing with dark creatures and dangerous situations. His knowledge and abilities can give Hermione a sense of security.