That the First Amendment calls for a truce is obvious. When it comes to religion (and non-religion), there are many potentially warring factions, for even though there is essentially only
one non-religion, there's a big raft of religions. And the first clause (the one that guarantees freedom
from religion) doesn't protect just the non-religious (
from religion generally); it also protects the followers of the various religions from each other's religion (
from religions particularly).
Episcopaleans, for example, are fully as happy as I am not to have to indulge Evangelicals or Jehovah's Witnesses (or anyone else who "reads the Bible literally"). And the really true-believing religionists, of course, are generally happy not to have any truck with those agnostic or (horrors!) even atheistic Unitarians and Episcopaleans. And many Americans, including religious Christians and Jews as well as the non-religious, are a little jumpy right now about Muslims, not least because many of even the most religious-sounding Christians don't
really take their religion quite as seriously as really believing Muslims do (probably not even Mitt Romney). (
Islam after all means "submission [to God]," and
Muslim "one who surrenders [to God].") And, of course, American Muslims are reciprocally a little uneasy living in a country whose current "president" (born-again, no less) talks about crusading in the Middle East. (Muslims who aren't Americans are a little uneasy about that too. Bush of course would remind us—since he no longer has Gonzales to do it—that
those Muslims aren't protected by our Constitution....)
So, the first clause protects everybody (who is covered by the Constitution).
Whom does the second clause protect? It says, "Congress shall make no law...prohibiting the free exercise [of religion]." Since the non-religious don't "exercise religion," they have nothing for the second clause to protect. (Their interest in the First Amendment comes back into play in the third and following clauses.) So, the second clause is there to protect the religious, that they may go about "exercising" their religion "freely."
But what does "free exercise" mean? It must, of course, at least exclude actions that nullify the first clause....
