Fr. Richard John Neuhaus has been writing an outstanding series on the primacy of the free exercise clause of the First Amendment. 

Once we forget that no-establishment is a means and instrument in support of free exercise, it is a short step to talking about the supposed conflict or tension between the two provisions. And from there it is a short step to the claim, as it has been claimed in numerous court decisions, that the two parts of the religion clause are “pitted against one another” and must somehow be “balanced.”

And from there it is but another short step to the idea that the no-establishment provision protects “secular liberty” while the free exercise provision protects “religious liberty.” When the religion clause is construed according to this curious inversion, it is no surprise that religious liberty comes out the loser. Any impingement of religion upon public life is taken to violate the secular liberty of the non-religious. Thus has no-establishment become the master of the free exercise that it was designed to serve.

Full article here.

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