Why did John Locke make exceptions to religious toleration for Catholics and atheists?

In his work A Letter Concerning Toleration, John Locke argued that religious toleration should be limited when beliefs or the lack thereof threaten civil authority or the stability of civil society.1

Locke’s exceptions were based on the following justifications:

• Roman Catholics: Locke viewed their allegiance to the pope—whom he considered both a spiritual and a political authority—as a direct challenge to the sovereignty of secular rulers and the autonomy of the English state.12
• Atheists: Locke believed that because atheists did not believe in God, they could not be trusted to uphold the sanctity of oaths, promises, or covenants, which he viewed as the essential bonds of human society.1

For Locke, the primary purpose of government is the protection of "civil interests," such as life, liberty, and property. Consequently, he argued that any group whose principles undermined the state's ability to maintain order or enforce contracts fell outside the scope of his proposed religious toleration.1