In his Letter Concerning Toleration, Locke gives three specific considerations to demonstrate that the power of the civil government
neither can nor ought in any manner to be extended to the Salvation of Souls.
First, each person is individually responsible for their own religious well-being:
[N]o man can so far abandon the care of his own Salvation, as blindly to leave it to the choice of any other, whether Prince or Subject, to prescribe to him what Faith or Worship he shall embrace.
If it is someone else's job to require you to follow a certain religion, then you are not attending to it yourself, and thus are not truly sincere.
Secondly, the power of the government
consists only in outward force: But true and saving Religion consists in the inward persuasion of the Mind; without which nothing can be acceptable to God.
If someone disobeys the government, it can only punish them externally, which does not change the mind and heart:
Confiscation of Estate, Imprisonment, Torments, nothing of that Nature can have any such Efficacy as to make Men change the inward Judgment that they have framed of things.
Finally, if governments in general could enforce belief, what would happen if a government enforced false belief?
For there being but one Truth, one way to heaven; what hopes is there that more Men would be led into it, if they . . . were put under a necessity to quit the Light of their own Reason; to oppose the Dictates of their own Consciences; and blindly to resign up themselves to the Will of their Governors . . . ?
Locke believed that Christianity was the single true faith, and that reason and conscience would naturally lead people to it. Thus, civil government should not put barriers to this, but allow individuals in every nation to follow reason and nature in order to reach the truth.