"During the Reformation, struggles between Protestants on one side and the Catholic Church on the other threw into high relief the often opposing claims of conscience and political obedience, and moved the question of obedience near the center of the polemical wars ongoing from the time of Luther to the time of Milton," (Yachnin 35).
Stephano: "Flout 'em and cout 'em/And scout 'em and flout 'em!/Thought is free," (Shakespeare III.2.133-35).
I just found this statement from Yachnin, though only historical background information, very profound when I related it to The Tempest. Perhaps Shakespeare was trying to send a message to his audience members about his own feelings on the political/religious controversies of his time by having Stephano sing, "Thought is free." Shakespeare was saying "To each his own," or something equally cliche, but he said it better by hiding his true meaning within the lines of his play.