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"Who are they?"
"The Guardians of the Whills. Protectors of the Temple of the Kyber. But there's nothing left to protect, so now they're just causing trouble for everybody."
― Jyn Erso and Captain Cassian Jeron Andor
The Guardians' priority is to resist the Empire and protect the people of Jedha.
Why would a rebel captain think otherwise?
This is addressed in the novelisation which contains a few extra lines of dialogue. In short, the Guardians are zealots. Although their cause is roughly aligned with the Rebellion, they're unreliable and likely to bring down Imperial attention.
She frowned. “What kind of trouble?”
Cassian turned his head in a slow arc as if checking for pursuit. “For the Guardians, anyone who’s not a pilgrim is intruding on holy ground. The Empire calls them strays…used to be domesticated, still beg for scraps, but they’ve really gone feral. Look at them wrong and they’ll bite your hand in a second.” “You’ll make me like them,” Jyn said.
She tried to push their faces, Chirrut’s voice, out of her brain. They probably were con men, even if they’d been zealots once. Beyond that, she didn’t know enough about the local religions to speculate; pilgrims from a hundred faiths came to the moon from across the galaxy, and all of them blurred together into the same pathetic cult, chanting and moaning and squirming under the Empire’s boot.
