The treatment of Tituba, the slave, is probably the most obvious example. While it's not surprising that tolerance of slaves did not really exist in the 17th century colonies, her treatment at the hands of her questioners is pretty telling. They are intolerant of any religion other than Puritan Christianity, so of course Tituba's practice of voodoo, in secret with the girls, is not going to be tolerated on any level. She is beaten for a confession, which she offers.
The Puritans were not tolerant of dancing either, or anything that could be construed as being of the Devil, or inherently sinful.