In the fanfiction world, Harry could be disillusioned with the Hogwarts system. Maybe he thinks the teaching methods are old - fashioned or the rules are too strict. He may believe he can learn more about magic on his own or in a different environment and thus doesn't want to go to Hogwarts.
Perhaps he has seen a dark future for Hogwarts in a vision. He might think that by staying away, he can avoid that future or protect himself from some unknown danger. In fanfiction, there are often new and creative plotlines like this.
One reason could be that he has fallen in love with someone outside of Hogwarts and wants to stay with that person instead. He may feel that Hogwarts will keep him away from his beloved.
One possible reason could be that in the fanfiction, his family might have decided to keep him away from the wizarding world for his safety. Maybe they feared the dark forces at Hogwarts, like Voldemort's followers.
In this fanfiction, it could be that Harry has a falling - out with Dumbledore or other important figures at Hogwarts. This makes him feel unwelcome or betrayed, leading him to choose not to go to Hogwarts and seek another path in the magical world.
One reason could be that he wants to experience a normal life. In the wizarding world, he is constantly in the spotlight as 'The Boy Who Lived'. At a Muggle school, he might be able to blend in and just be an ordinary kid for once.
One reason could be a prophecy. In the wizarding world, prophecies often drive events. Maybe there's a new prophecy that says Harry must be at Hogwarts at a certain time for some great event to occur. So, the magical community, in an effort to fulfill the prophecy, forces Harry to go. It's like they are trying to shape the future according to the words of the prophecy.
One possible reason could be fear. Maybe he's heard some scary rumors about Hogwarts, like the Forbidden Forest being full of dangerous creatures. Another reason might be that he doesn't want to leave his normal life behind. He has friends in the Muggle world and he might be reluctant to give that up for a world full of magic that he doesn't fully understand yet.
One reason could be that he doesn't like others taking creative liberties with his story. He might feel that it's his story and only the original version should be the 'true' one.
One possible reason could be a dark turn in the story. Maybe Harry is under the influence of a dark magic or a powerful and evil entity that makes him lose control and start to destroy Hogwarts. For example, if he was possessed by a powerful dark spirit that wanted to eradicate the symbol of the wizarding world's good, which is Hogwarts.
In some fanfictions, there could be a change in the Hogwarts admission policy. Maybe they found some supposed flaw in Harry's magical abilities or his background that led to his admission being revoked at the last minute, so he didn't arrive at Hogwarts. Also, it's possible that some other powerful magic was at work. A powerful wizard or witch could have cast a spell on Harry that made him forget about Hogwarts or made it so that he couldn't physically reach the school.
One possible reason could be that he was under the influence of a powerful dark magic or a curse that made him lose control. Another reason might be that he was tricked into believing Hogwarts was a threat to the wizarding world in some extreme way. Maybe a powerful enemy manipulated him to think that destroying Hogwarts was the only way to save everyone.