The inhabitants feel the need of an innate air of resistance to get rid of the witches.
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The quote is actually:
To the best of their knowledge the American forest was the last place on earth that was not paying homage to God. For these reasons, among others, they carried about an air of innate resistance, even of persecution.
The puritans were used to being persecuted. They knew about resisting even common sense for their beliefs. They feared change and would fight to keep their existing beliefs.