Maybe he feels betrayed. In the original story, Naruto has faced a lot of discrimination in Konoha when he was young. So in the fanfiction, it could be that some similar or new issues make him decide to hide.
It could also be that he has some secrets that he doesn't want Konoha to find out. These secrets might be related to his new powers or some past events that he fears will cause chaos in Konoha if revealed.
He might be trying to protect Konoha in his own way. He could have discovered some kind of threat that he believes he can only deal with by staying away and hiding from the village so that the enemy won't target Konoha directly because of him.
Well, in fanfictions, often the plot takes a different turn. Naruto might hide from his family because there could be some sort of misunderstanding. For example, there could be false rumors about him being involved in something bad. And he might think that his family would believe those rumors without giving him a chance to explain. So, to avoid the immediate confrontation and judgment, he chooses to hide.
It could be that Konoha wants Naruto to use his influence to bring peace among different clans. Naruto is well - liked and respected, and his words might carry a lot of weight.
Another aspect could be related to past traumas. Naruto has been through a lot, and if the Konoha 11, even unintentionally, reminded him of some of the negative experiences he had in Konoha, like the ostracism he faced as a child, it could make him hate them in the fanfiction.
In some fanfictions, Naruto might be depicted as hating Konoha due to feeling betrayed. For example, if the village turns against him unjustly or fails to support him when he needs it most. Maybe they suspect him of something he didn't do, like being involved in a crime against the village, which could lead to his hatred.
Well, in some fanfictions, Naruto might outsmart Konoha by using his unique knowledge of the village's secrets that others don't know. For example, he could use his understanding of the old tunnels under Konoha to his advantage in a situation where he needs to escape or gain an upper hand in a conflict.
Maybe he has some personal grudges against the village. For example, he might have felt betrayed by the village in the past and that made him reluctant to offer help.
One reason could be that he feels misunderstood by the villagers. Despite all he has done for Konoha, some still hold grudges or are afraid of his power. Another might be that he wants to explore the world on his own terms, away from the responsibilities and restrictions of Konoha. Maybe he also feels a sense of loneliness there, as he has lost many important people and the village constantly reminds him of those losses.
Because Naruto is like a beacon of hope for them. He's always been the one to inspire them, so they feel the need to protect him in return.
Perhaps she witnessed some dark secrets of Konoha that made her lose faith in the village. It could be something related to the way the village leadership handled certain events or treated some of its people unfairly.
Konoha could be interested in the creativity of the fanfiction writers. They take the elements from Naruto and RWBY and create something entirely new. For instance, they might give Naruto the ability to use RWBY - style magic, or have RWBY characters learn ninja techniques. Reading these fanfictions allows Konoha to see the different ways the two universes can be merged. Also, it could be that Konoha wants to see how the characters from both series would interact in different scenarios that the original works don't cover.