The main point that I got from Locke's Letter of Toleration comes from chapter 4. It talks about the limit of toleration between individual people. Simply put, it talks about toleration (shocking I know) for someone else's beliefs. Particularly, it's about how it is wrong to encroach on someone else's rights, or even harm that person, purely because of their differing beliefs. The last sentence in particular sticks with me: "if someone strays from the right path, that is his misfortune, not yours; and your belief that he will be miserable in the after-life is not a reason to give him a bad time in his present life." He just says to agree to disagree and to treat them no differently than you would someone who shares your beliefs. He even makes the argument that the gospel teaches kindness and charity.
Edit: Commented on Stephen Davis' and Gray Moore's posts
Edit: Commented on Stephen Davis' and Gray Moore's posts
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Nice post Logan!