Richard W. Garnett writes in Public Discourse about how the separation of church and state protects the freedom of conscience:
…[H]ow, precisely, do the anti-establishment norm and the “separation of church and state” vindicate the freedom of conscience? We know that Roger Williams—the founder of the colony of Rhode Island and a fierce and fiery critic of the “soule rape” of religious persecution—connected the protection of conscience with the maintenance of a wall between the “Garden” of religious faith and the “Wilderness” of civil power and public affairs. But again, how exactly does this wall, this separation, protect the “soule,” the seat of conscience?
The “separation of church and state,” it turns out, is a powerful structural principle; it is a principle of pluralism, of multiple and overlapping authorities, of competing loyalties and demands. It is a rule that limits the state (not a program of marginalizing or privatizing religion) and thereby clears out and protects a social space, within which persons are formed and educated, and without which the liberty of conscience is vulnerable. The no-establishment rule, then, protects the liberty of conscience primarily by respecting and protecting the independence of non-state authority.
Read the full article here.