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The first amendment bundled parts of several key civil rights together. They were not limited to how the people interacted with government; they were focused on how the people interacted with each other. Remember that prior to the Revolution, British soldiers would stand on street corners watching the people for signs of subversive behavior. The first amendment was to guarantee to the people that the new government would never do this.

The first Congress undertook the exercise to draft the Bill of Rights amendments to the Constitution. Here is the text of now-Representative James Madison's first draft of what would become the first amendment submitted to the 1st Congress House of Representatives:

The civil rights of none shall be abridged on account of religious belief or worship, nor shall any national religion be established, nor shall the full and equal rights of conscience be in any manner, or on any pretext, infringed.
The people shall not be deprived or abridged of their right to speak, to write, or to publish their sentiments; and the freedom of the press, as one of the great bulwarks of liberty, shall be inviolable.
The people shall not be restrained from peaceably assembling and consulting for their common good; nor from applying to the Legislature by petitions, or remonstrances, for redress of their grievances.

Notice that in #4, Madison wrote "The civil rights of none shall be abridged" not "Congress shall make no law."

A House committee was formed to streamline Madison's language, and they came up with this:

No religion shall be established by law, nor shall the equal rights of conscience be infringed.
The freedom of speech, and of the press, and of the right of people to assemble and consult for their common good, and to apply to the government for redress of grievances, shall not be infringed.

Notice that the committee removed the part about the free exercise of religion. During debate, members of the House further revised #3 to be this:

Congress shall make no law establishing religion, or to prevent the free exercise thereof; or to infringe on the rights of conscience.

The House finally approved 17 amendments to be sent to the Senate. The final House-approved text for the future first amendment became this:

ARTICLE THE THIRD.
Congress shall make no law establishing religion, or prohibiting the free exercise thereof; nor shall the rights of Conscience be infringed.
ARTICLE THE FOURTH.
The freedom of Speech, and of the Press, and of the right of the People peaceably to Assemble, and consult for their common good, and to apply to the Government for a redress of grievances, shall not be infringed

Now the Senate began streamlining the proposed amendment from the House, eventually revising the list down to 12 amendments. The first amendment, which began as three separate amendments, then revised to two, and then submitted to the states as the third overall amendment, finally became this:

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.

Based on the nature of the revisions, it doesn't appear that the "separation of church and state in our system of government, a tenet of the First Amendment known as the Establishment Clause" was ever a concern. In fact, the focus seemed to about protecting the "civil rights" of the people to worship as they pleased.

It's interesting to note that Madison originally put protecting the civil right to worship ahead of preventing the establishment of a national religion. The Senate reversed this sequence, perhaps for style over any overt reasons.

-PJ