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 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.
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 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.
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.
Romance is a prevalent theme as well. The relationship between the faunus oc and one of the RWBY characters can be a central part of the story. It could be a slow - burn romance, starting from initial distrust or rivalry and gradually developing into love. Writers often use this theme to add emotional depth to the story and show how different personalities can come together.
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 is the character who has been expelled, so he is central to the plot. His character might be dealing with feelings of betrayal, confusion, and a desire to clear his name. The OC, on the other hand, could be a very unique individual. They might have their own goals and motives that initially seem separate from Jaune's situation. But as the story progresses, their paths become intertwined. For example, the OC could be a healer who decides to help Jaune because they sense his innocence, and their relationship develops from there.
A possible plot twist could be that Ruby is actually a long - lost heir to a powerful Faunus clan, and Weiss's family has some hidden connection to this clan's past. When this is revealed, it completely changes their dynamic as they have to re - evaluate their relationship and the roles they thought they had.