One possible reason could be lack of understanding. If Jaune X has grown up in an environment where Faunus are misrepresented or he simply hasn't had much interaction with them, he might be scared. For example, if all he has heard are horror stories about Faunus being dangerous, he would naturally be afraid.
Another way is that his fear could be exploited by some antagonist in the story. They might use his fear to manipulate him into doing things against the Faunus. This would create a lot of conflict and drama in the fanfiction. As the story progresses, Jaune X might then realize he has been used and start to change his view of the Faunus.
One possible plotline could be that Jaune has been hiding his Faunus identity to avoid discrimination. As the story progresses, his secret might be revealed during a crucial event, like a battle where his Faunus abilities give him an edge.
One reason could be Kakashi's Sharingan. It's a very powerful and somewhat spooky ability. Naruto might see it in action in a way that scares him. Maybe Kakashi uses it to subdue an enemy in a really intense way that makes Naruto realize how dangerous Kakashi can be.
I'm not sure of a specific 'jaune is secretly a faunus fanfiction' to recommend. You could try searching on fanfiction platforms like Archive of Our Own or FanFiction.net.
One possible reason could be Kakashi's reputation as a strict and powerful teacher. Naruto might be in awe of his skills and fear making mistakes in front of him.
Lucius' power within the dark wizarding world could be intimidating to Draco. He has connections, influence, and a certain level of magical ability. Draco might be scared that if he steps out of line, Lucius could use his power against him, or even put him in danger. Also, Lucius' cold and often unforgiving demeanor could make Draco feel constantly on edge in a fanfiction.
In a fanfic, Sasuke's association with dangerous elements might make Sakura scared. For instance, if he teams up with a group of rogue ninjas. Also, his emotional state could play a role. If he is consumed by revenge and his anger is constantly boiling over, Sakura, who cares about him, might be scared of his self - destructive tendencies. Additionally, if Sasuke were to develop some sort of mind - control ability that he struggles to control, Sakura would surely be frightened.
It could be that Jaune has some sort of traumatic past experience with funus, which makes him scared. Maybe he witnessed its destructive power or had a personal encounter that left him with deep - seated fear.
Jaune could be a character created specifically for this fanfiction. Maybe he's a hero - in - the - making who is just starting to discover his abilities but is held back by his fear of funus.
One possible plot could be that they are in a spooky dungeon during a mission. Noelle is scared of the dark and the unknown creatures lurking. Asta, being his brave self, tries to comfort her and protect her. As they face different challenges, their relationship deepens.