Ten of the original 13 colonies had official (“established”) state religions, including Anglicanism, Congregationalism and Protestant Christianity in general. Under the First Amendment, the states remained free to designate official state churches. States could levy taxes in order to support the official state church, pay its ministers and build and maintain its meeting-places. So far as the First Amendment was concerned, states could discriminate against all forms of religion other than their own established churches. (Some states themselves passed laws that prohibited these things and they were free to do that as well.)
But whatever individual states might do, the First Amendment said that the federal Congress — the law-making branch of the national government — could neither promote one form of religion above another (the Establishment Clause) nor hinder any particular religion (the Free Exercise Clause).