Another reason could be a misunderstanding. Maybe he overhears something Harry and Hermione say and misinterprets it as them not wanting him around anymore. So, in a fit of anger and hurt, he leaves. This can lead to a lot of angst and drama in the fanfiction as the other characters then have to figure out how to get him back.
In some fanfictions, Ron might leave because he has a family emergency back home. His family might be in danger, and he feels the need to go back to protect them. This could also be a way for the author to explore Ron's loyalty to his family and how it competes with his loyalty to his friends.
Well, perhaps in the fanfiction they leave because of a prophecy. A prophecy might state that their presence near Hermione would bring great danger to her or to the wizarding world as a whole. So, they sacrifice their friendship and leave. Also, it could be due to some dark magic influence. They are forced by a powerful dark magic spell to stay away from Hermione, not having control over their actions.
In the fanfiction world, it could be a prophecy. There might be a prophecy that says Harry's presence in Ginny's life will bring great harm to her or the wizarding world. So, for the greater good, Harry leaves. He believes that by sacrificing his relationship with Ginny, he can save her and everyone else. It's a very noble but also a very heart - breaking decision.
One possible reason could be a plot device to create drama. By having Harry ignore Ron, it can lead to tension within their friendship, which is a central relationship in the original series. This can then drive the story forward as they have to resolve this issue.
Perhaps there were some secrets that Ron was keeping from Harry. In the wizarding world, secrets can be a big deal. If Ron had a secret related to his family or some other important matter and Harry found out about it in a way that made it seem like Ron was hiding something bad, it could lead to Harry not trusting him. Also, Ron's friendship with other characters might make Harry jealous or suspicious. If Ron was getting closer to someone Harry didn't trust, it could spill over and make Harry question Ron's loyalty to him.
One reason could be a falling - out with his friends in Gryffindor. Maybe there was a misunderstanding that grew so large that he felt he couldn't stay. Another possibility is that he might be lured away by some mysterious force or character who convinces him that Gryffindor is no longer the right place for him. For example, if a new group claims to have a better way to fight Voldemort and they are from a different 'house' in this fanfiction concept.
One reason could be that Ron abandons Harry when he needs him the most. Like in a dangerous situation, if Ron runs away leaving Harry alone to face the threat, Harry would find it hard to forgive such cowardice.
One possible reason could be that Harry discovers some secrets about Dumbledore that make him lose trust. For example, if he finds out about Dumbledore's past mistakes or hidden agendas that he doesn't agree with. Another reason might be that Harry feels he can better protect his friends and fight Voldemort on his own terms, away from Dumbledore's influence and strategies which he may start to question.
In some fanfiction, Harry leaves to seek more powerful magic. He realizes that the magic in Britain is somewhat limited in the fight against Voldemort. So he travels to other places, like ancient magic - rich regions in Asia or Africa, to find a way to defeat Voldemort. He hopes that by leaving, he can gain the upper hand in the battle.
Maybe he's tired of the spotlight in England. In some fanfictions, he could be seeking a new start away from the prying eyes and the constant media attention that comes with being in England.
One possible reason could be a major disagreement with the Gryffindor house leadership or some of the students. Maybe he feels that they are not living up to the values he thought they held. Another reason might be that he discovers some dark secret within Gryffindor that makes him uncomfortable and he decides to leave.