In his book Revolutionaries: A New History of the Invention of America(p. 307), Jack Rakove writes:

As he later explained in Notes on the State of Virginia, Jefferson had further reasons for making historical literacy the foundation of a common education. Rather than “putting the Bible and Testament into the hands of the children, at an age when their judgments are not sufficiently matured for religious enquiries, their memories may here be stored with the most useful facts from Grecian, Roman, European and American history.” … the kinds of historical facts that Jefferson deemed useful and his ideas of education carry over into the subject of bill 82, the bill for religious freedom. Though its formal purpose was to disestablish the Anglican Church, its deeper animus was to free individuals from any obligation to adopt religious views they found unpersuasive. In Jefferson’s view, all religious belief was finally a matter of individual opinion. The history of religious establishments was an unrelenting story of corrupting alliances between churchmen and rulers, abusing their power to impose their opinions and modes of thinking on others. This too was a form of tyranny, as inimical to liberty as anything else the Stuarts and other execrable autocrats had attempted. For Jefferson as for Locke, religion was not  a matter of children inheriting the faith of parents. It was instead a subject of inquiry, and no one could simply adopt another’s convictions. The point of reading history first, scripture later, was to empower individuals to judge the claims of all religions by teaching them that much of what passed for orthodoxy in other times and places depended on the impure alliance of church and state.

See also “The Importance of the Next Generation: Thomas Jefferson Grokked It.”