One possible reason could be that in the fanfiction, Hermione might be more focused on her studies or magical research. She has always been an academic at heart, and perhaps she feels that a sexual relationship with Ron would distract her from her intellectual pursuits.
It could also be due to her personal growth and self - discovery. Maybe she realizes that she's not ready for that kind of physical intimacy with Ron. She might be exploring her own identity and independence, and a sexual relationship doesn't fit into her current view of herself and her relationship with Ron. For example, she could be on a journey to become a more powerful witch first and doesn't want any romantic or sexual entanglements to hold her back.
Another aspect could be related to the way the author of the fanfiction wants to portray their relationship. The author might be aiming to add more depth and complexity to their relationship by introducing this element of Hermione's refusal. It could be a way to show that their relationship isn't just about physical attraction but also about mutual respect, friendship, and shared values. And Hermione's refusal might be a way to test Ron's understanding and patience in the relationship.