Why did the Pueblo revolt against the Spanish missionaries in New Mexico?

because the Spanish had infected their villagers with deadly smallpox

Explanation:

Diseases brought by the Spanish Settlers, such as smallpox and typhus, had already wiped out several Pueblo villages, so their numbers were fast dwindling.  Alarmed that their traditions and customs would soon fade away, the Pueblo chiefs, under a leader named Po'pay, decided to mobilize their warriors and attack the Spanish.

unless they converted, many non-christians (mainly jews and muslims) were persecuted

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