Maybe he has some unresolved issues from his past. For example, the trauma of his parents' death and his difficult childhood might make him hesitant about starting a family. He could be worried that he wouldn't be a good husband or father. Also, in the fanfiction, he might have a different calling or mission that he believes would be compromised if he got married to Ginny. He might think that his relationship with Ginny would limit his ability to pursue certain things he feels are important.
One possible reason could be that he might fear for Ginny's safety. In the wizarding world, there are always threats from dark forces. Harry has already lost many people he loves, and he might not want Ginny to be in more danger because of their relationship. Another reason could be that he wants to focus on his own personal growth and exploration. Harry has spent so much of his life fighting Voldemort and dealing with the wizarding world's problems that he may feel he needs time alone to figure out who he really is without the added pressure of a marriage.
It could be that he has seen some flaws in their relationship. Perhaps they have different long - term goals or values. Ginny might be more interested in a traditional wizarding family life, while Harry could be more drawn to a life of adventure and exploration in the wizarding world. Their different desires could lead Harry to avoid marriage. Also, he might be influenced by the opinions of others around him, such as his friends or other members of the Order of the Phoenix, who might unknowingly plant doubts in his mind about marrying Ginny.