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.
Well, Jaune in RWBY fanfiction can vary a lot. Sometimes he's the underdog who overcomes huge challenges, and other times he might have unique powers or a special backstory.
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.
It could be because Jaune is a relatable character. He starts off as a bit of an underdog in RWBY. So, fans like to write stories where the other characters notice his potential and become obsessed with him as he grows.
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 really like 'Weiss and the Faunus Bond'. In this fanfiction, Weiss discovers the unique aspects of Faunus culture through her interactions. It shows her growth as a character as she overcomes her initial prejudices. It also has some great action scenes intertwined with the emotional development.
Faunus in Naruto and RWBY fanfiction can be used to explore themes of discrimination. In RWBY, Faunus face discrimination, and this can be paralleled in the Naruto universe. Fanfiction might show Faunus being treated like the Jinchuriki or the Uchiha clan, who were also ostracized. They could be fighting for equality in the Hidden Leaf Village or other ninja villages, just like they do in RWBY's Vale or other kingdoms.
The theme of unity also pops up frequently. Some fanfictions show how faunus and humans can come together despite their differences. They might fight a common enemy or work towards a common goal. This is important as it shows that the two groups can coexist and even thrive when they put aside their differences.
There's this fanfiction called 'Faunus - Pyrrha's Secret'. It tells a story where Pyrrha has been secretly helping the Faunus all along. It's full of mystery and intrigue as the other characters start to suspect that Pyrrha is up to something related to the Faunus. The character development in this one is really well - done.