This essay is an historical look at the origin of the doctrine of political "rights," in particular the natural "unalienable rights" of "conscience," which in turn gave rise to religious rights.
Earlier while discussing this issue with Matt Scofield I noted a parallel development of the rights of conscience, that this doctrine literally was a cooperative project between Protestant dissidents and Enlightenment rationalists.
The rights of conscience doctrine developed because there was a need to "solve" the "religious problem" of bloody persecution that so plagued the West before liberal democracy emerged as the dominant form of government. To be sure, Protestant dissidents got the ball rolling and started calling for religious toleration before the Enlightenment. For instance, Roger Williams in 1644, well before Hobbes and Locke, famously wrote:
All civil states with their officers of justice, in their respective constitutions and administrations, are . . . essentially civil, and therefore not judges, governors, or defenders of the Spiritual, or Christian, State and worship. . . . It is the will and command of God that, since the coming of His Son, the Lord Jesus, a permission of the most Paganish, Jewish, Turkish or anti-Christian consciences and worship be granted to all men, in all nations and countries; and they are only to be fought against with that sword which is only, in Soul matters able to conquer, to wit; the sword of the Spirit--the Word of God. . . . God requireth not an uniformity of religion to be enacted and enforced in any civil state; which enforced uniformity, sooner or later, is the greatest occasion of civil war, ravishing consciences, persecution of Christ Jesus in His servants, and of the hypocrisy and destruction of millions of souls. . . . An enforced uniformity of religion throughout a nation or civil state confounds the civil and religious, denies the principles of Christianity and civility, and that Jesus Christ is come in the flesh.
A few important notes on Williams: First, as I learned from Philip Hamburger, it's unlikely that Roger Williams cared at all about the welfare of those being persecuted but rather had a fanatical desire to keep the Christian Religion "pure" from "corrupt" world influences, of which civil government was certainly one. Second, keep in mind that Williams's sentiments were absolutely novel and anomalous for his time and didn't really catch on until later. And third, notice how Williams phrased his words: "a permission [my italics] of the most Paganish, Jewish, Turkish or anti-Christian consciences and worship be granted to all men, in all nations and countries...." Today, or even one hundred and some odd years later in the 18th Century, we would instead assert "a right, or an unalienable natural right, of the most Paganish, Jewish, Turkish or anti-Christian consciences...." Williams did not use the word "right," "unalienable" or otherwise to describe religious freedom/toleration, but rather "permission." Now, Williams did not purposefully avoid using that word, but rather (interestingly) at that time, no one had yet begun speaking in the language of rights which governments were in the business of securing.
[Note: This is something I learned from Allan Bloom, and the other Straussians. Their interpretations of history and philosophy have been criticized from both the left and the right and they do endorse the controversial notion that philosophers wrote in code and could say one thing while meaning another. Therefore, when they make a claim, it's best for the reader to go to the primary source, read it in its context and decide for him or herself whether the Straussians are right. And although I'm not an expert reader of manuscripts, nothing that I have uncovered has contradicted the following Straussian theory which I am about to explain].
So when did we start speaking in language of "political" rights? Allan Bloom in The Closing of the American Mind explains:
[Enlightenment] provides the structure for the key term of liberal democracy, the most successful and useful political notion of our world: rights. Government exists to protect the product of men's labor, their property, and therewith life and liberty. The notion that man possesses inalienable natural rights, that they belong to him as an individual prior, both in time and in sanctity, to any civil society, and that civil societies exist for and acquire their legitimacy from ensuring those rights, is an invention of modern philosophy. Rights...are new in modernity, not a part of the common-sense language of politics or of classical political philosophy. Hobbes initiated the notion of rights, and it was given its greatest respectability by Locke. p. 165
Thus, the notion of the social contract, that governments are in the business of securing individual rights is a Hobbsean notion. Locke gave "rights" their greatest respectability because Hobbes was not an orthodox Christian and his theory challenged the existing order -- divine right of Kings -- defended most notably by Filmer on explicitly orthodox Christian grounds. It was Locke who successfully argued (rightfully or wrongfully) to a Christian audience that the notion of "rights" and the social contract was perfectly compatible with Christianity.
This is why the Straussians understand Locke to be a "Hobbsean"-Locke, because he took Hobbes's (seemingly un-Christian) ideas and made them palatable to a Christian audience.
Thus, when thinkers like Jefferson and Madison speak of "unalienable rights," even God-given unalienable rights, they are speaking in an Enlightenment language and in Hobbsean-Lockean terms. The theory of "natural law" on the other hand, is quite ancient and traces back to Aristotle and was adopted into Christendom by Aquinas. The theory of "natural rights," as we have seen, is a modern-Enlightenment notion. Natural law and natural rights, however, are both supposed to be "self-evident Truths" ascertainable to man as man, through his unaided Reason. (If one believes that natural law and natural rights are the objective immutable Truth, we could say that "natural rights" were a much later "discovery" than natural law.)
The three documents which best encapsulate America's foundational notion of "natural rights," specifically, natural religious rights, are the Declaration of Independence, Madison's Memorial and Remonstrance, and Jefferson's Virginia Statute for Religious Freedom.
Note though, a populace composed primarily of Christians (many of them orthodox) signed onto the Enlightenment theories espoused in these documents. Indeed, many orthodox Christians adopted in their arguments the language of natural rights. For instance, the Baptist leader John Leland, in 1791 could write pamphlets like the one entitled The Rights of Conscience Inalienable, and Therefore, Religious Opinions Not Cognizable by Law.
[Note: Allan Bloom talks about this phenomenon where he discusses the power of language and that the post-Nietzschean language of "value relativism" had altered the way we think of ourselves by seeping into not only the vocabulary of the friends of relativism, but also its enemies, and into the language of the common American man. For instance, the term "values" itself -- a creation of German nihilists -- implies the relativity of Truth. Therefore, when Christian Conservatives use terms like "Family Values" or "Traditional Values," they have already ceded to the relativists, so Bloom's theory goes. Ironic though that Straussian Bill Kristol, who himself was intimately familiar The Closing of the American Mind, helped coin the term "Family Values" when he worked for Dan Qualye. I guess it flowed better than "Family Virtues."
Anyway, Bloom's passage on this is as follows:
When Bishops, a generation after Hobbes's death, almost naturally spoke the language of the state of nature, contract and rights, it was clear that he had defeated the ecclesiastical authorities, who were no longer able to understand themselves as they once had. pp. 141-2.]
And indeed, even though the theory holds that natural rights are granted by [Nature's] God, the Bible nowhere speaks of "unalienable rights" which governments are in the business of securing. Therefore the Declaration of Independence, Memorial and Remonstrance, and Virginia Statute on Religious Freedom are not "Christian" documents espousing a "Biblical" creed, but rather Enlightenment documents which are compatible with certain forms of orthodox and unorthodox Christianity, and let us not forget, also incompatible with certain forms of orthodox Christianity.
This is why, I think, the Straussians argue that Locke was trying to "secretly" subvert revealed Christianity: The Declaration, Memorial and Remonstrance, and Virginia Statute are all incompatible with (at least one important feature) of the dominant, traditional understanding of orthodox Christianity up until that time. Traditionally, both Catholicism and orthodox Protestantism (ala John Calvin and John Winthrop, men who knew the Bible as well as anyone else) made little or no distinction between Church and State and frequently violated the unalienable rights of conscience. Calvin, as governor of Geneva, had one of his Unitarian critics, Michael Servetus, put to death for publicly questioning the Trinity, and Winthrop as leader of Puritan Massachusetts (like most other colonies) attempted to incorporate the entire Bible into the civil codes, even and especially all of those sections where the "Jealous" God of the Bible forbids the worship of false Gods. In those colonies (all but Roger Williams's Rhode Island) non-Christians merited punishment, often the death penalty, for publicly practicing their religion (as the Old Testament dictates).
Keep in mind the First of the Ten Commandments: Whereas the Jealous God of the Bible forbids the worship of any God but He, Jefferson's and Madison's "Nature's God" grants men an unalienable right to worship no God or twenty Gods.
Therefore, the Declaration and its cognate documents are simply not compatible with Winthrop's or Calvin's understanding of Christianity, or with what the Catholic Church's understanding was up until that time. However, these documents were entirely compatible with Roger Williams's (what was, in Williams's time, novel and anomalous) understanding of Christianity (which was, to be fair, fanatically orthodox). In time, Williams's understanding of the Bible and "the permission" of "Paganish, Jewish, Turkish or anti-Christian consciences" to freely worship became more dominant among Christians, especially among the dissidents. And that is why Enlightenment rationalists and Protestant dissidents could cooperate to create and establish the doctrine of "natural rights," in particular the "unalienable rights of conscience."