"...If there were no room for doubt, there would be no room for me...”

― Frederick Buechner

Taking the 17th Century English Protestant sect as a metaphor, "Puritans" is really about all sects and cults that operate on the edge of extremity, whether Christian; Muslim; Judaic; other.

Whether the wars waged by the Crusaders in the 11th and 12th century supposedly in the name of Christ; or the 2001 9/11 terrorist actions hijacking both planes and a claim to Islam.

It's about the danger of conviction. How anyone can possibly be so sure of themselves and their position that they would justify even the worst acts of barbarism?

Essentially, the song is a call for tolerance. For sober heads and thoughtfulness to prevail in the face of fanaticism.