Why do we treat a letter written by Jefferson as more constitutionally relevant than the actual Constitution?

Even if you are very religious, you should still want a separation of church and state to not have the government meddling with issues of your church, temple, synagogue, etc....I don't see how people who supposedly hate government and believe it is all corrupt would want something they cherish so deeply like religion to be connected to it. Regardless of how you interpret the establishment clause, it's better for everyone to have them separate and not meddling with one another.