In some fanfictions, it could be due to a prophecy or a magical bond that they discover. They might feel that the only way to fulfill the prophecy or strengthen the bond is by getting married secretly. Another aspect could be the political situation in the wizarding world. There could be political factions that would oppose their union for various reasons, such as Harry being seen as a symbol of a certain side and Fleur being from a different background. So, to avoid political turmoil or to keep their relationship safe from political manipulation, they choose to marry secretly.
One reason could be to protect the person he marries. If she's a commoner, for example, the noble society in Camelot might not accept their relationship. So, they keep it a secret. Another reason could be that the person he marries has some sort of power or identity that could put them in danger if it was known. For instance, if she was a sorceress, in Camelot where magic is feared, they'd have to marry secretly.
Maybe to protect her from his enemies. If his foes knew about her, they might target her.
One possible reason could be Fleur's unique charm. She is part - Veela, which gives her an alluring quality that might make Harry feel insecure. Another reason might be her skills. If in the fanfiction she is shown to be extremely talented in magic, especially in areas where Harry struggles, it could trigger his jealousy.
One possible reason could be differences in their personalities. Harry is often portrayed as more down - to - earth and Fleur as more haughty in the books. In fanfiction, this might be exaggerated, causing her to reject him. Maybe she doesn't like his fame either, as Harry is 'the Boy Who Lived' and always in the spotlight, which she might find tiresome.
One possible reason could be that Harry has seen so much death and destruction during the war that he is afraid of forming new, deep emotional bonds. He might worry that he could lose his loved ones again, so he refuses to marry as a way to protect himself from potential future heartbreak.
In a lot of these fanfictions, it could be that Harry has a secret mentor. This could be an old wizard who has been secretly guiding Harry in potions, away from the prying eyes of the Hogwarts staff. This mentor could have seen Harry's potential early on and decided to help him develop his skills in private. Another aspect could be that Harry's own determination and his need to prove himself in a different area other than Quidditch or fighting Voldemort drives him to secretly practice and become good at potions. Also, the idea that there are hidden aspects of magic within him, perhaps related to the founders of Hogwarts, that only manifest in his potions - making ability.
One possible reason could be that Harry is still haunted by his past traumas and feels he's not in the right mental state to marry anyone. His experiences with Voldemort and the losses he's endured might make him reluctant to bring Ginny into a potentially unstable future.
Maybe Harry has some unresolved issues from his past, like the trauma of losing his parents and many of his friends during the fight against Voldemort. These could make him hesitant to enter into a marriage with Ginny. He might also be worried about how the wizarding world would view their marriage, especially if there are still some who oppose him or his family.
In some fanfictions, Fleur might leave Bill for Harry because she realizes that Harry has a certain selfless quality that she admires more. Harry's constant fight against evil and his willingness to sacrifice himself could be very appealing to Fleur. Also, it could be that the fanfiction is set in a situation where Bill is involved in something that Fleur morally opposes, and Harry represents a more morally upright choice for her.
One possible reason could be a misunderstanding. Maybe Fleur misinterprets Hermione's actions as a threat to something or someone she cares about. So, she restrains Hermione to prevent her from causing further 'harm' until she can figure out what's really going on.