There's no reason a peaceful, animal-loving, shy gal couldn't be a Muslim. It's just that, well, Fluttershy isn't
a Muslim, and putting her in the Islamic Female Subjugation Hat is fucking shit.
The same would be true if you put her in nun regalia or made her shave her hair and wear a wig like overly-religious Jews. You can probably get away with giving ponies real-world religious beliefs if those beliefs manifest in private; that's the sort of subtle shit you can slip into a character without diverging too far from their real character. But she's fucking covering her hair because it's woman hair is shameful according to her patriarchal shit religion? How Equestrian of you.