By virtue of the first clause, the states and the people as such are protected from federal domination; by the second, individuals are protected from coercion in their religious conduct. The first clause allows the states and the people as such to follow their will in matters of religion; the second guarantees the same liberty to individuals and the corporate persons they voluntarily compose. The first has as its object matters that are decided by the will of the people (i.e., by the will of the constitutionally determined majority in the different states). The second involves matters decided by the will of each individual.
Parallel rights and actions
The failure to observe this distinction leads to the absurd presumption that all government action in matters of religion is somehow inherently a contravention of individual freedom. This can be no more or less true in matters of religion than it is in any other area in which both individuals and governments are capable of action and decision.
The government's power to arm soldiers for the community's defense does not inherently contravene the individual's right to arm himself against personal attack. The government's power to establish institutions of higher learning does not inherently contradict the individual's right to educate his young or join with others to start a school. The government's power to engage in economic enterprises (such as the postal service or electric power generation) does not inherently contradict the individual's right to private enterprise. It is possible for government coercively to inhibit or repress any of these individual activities, but it is obvious that government action does not in and of itself constitute such coercion.
As the U.S. Constitution is written, matters of religion fall into this category of parallel individual and governmental possibilities. Federal and state governments, in matters of religion, are forbidden to coerce or prohibit individual choice and action. Within the states, the people are free to decide by constitutional majority the nature and extent of the state's expression of religious belief.
This leaves individuals free to make their own choices with respect to religion, but it also secures the right of the people of the states to live under a government that reflects their religious inclination.