There are two ways to tell the story of how America (eventually) secured religious liberty in the First Amendment. Conventional wisdom in the scholarly realms is that secular Enlightenment figures—John Locke and the like—overcame religion with reason. So religious liberty was a victory for Enlightenment intellectuals. The other way to tell the story is that it was, in fact, religious folks who were the earliest champions for religious liberty—and not just for practical reasons (like to avoid persecution). They did it for theological reasons. Thus religious liberty was a victory for the Christian faithful of various stripes.
Nicholas Miller defends this second way of telling the story in The Religious Roots of the First Amendment: Dissenting Protestantism and the Separation of Church and State (Oxford, 2012). His thesis is that Protestants from Martin Luther on down to the time of the First Amendment held as a theological principle “the right of private judgment” in biblical interpretation and in religious matters. His book is an effort to trace this continuous thread across several continents and a couple hundred years. It is a great introduction to the heritage of liberty in the Protestant traditions. And it makes a compelling case that those same Enlightenment intellectuals may well have been influenced by dissenting Protestants.
Anyone interested in the origins of religious liberty in America will benefit from this excellent scholarship written very clearly. The introduction and appendix can bring you up to speed on the best current works on this topic. And it puts current religious liberty issues in very helpful perspective.