Most clergy in Jefferson’s lifetime were not antagonistic to him. Only later did this begin to be popular in some historical works of clergy.
And similarly Jefferson was not universally opposed to the clergy. His anti-clericalism was clearly selective and focused, and for biographers to not make that distinction is unfair to Jefferson. Indeed, those that fail to make the distinction become the allies of his political enemies. Jefferson’s understanding of religious freedom is held by the vast majority of American evangelicals to this day. We do not favor a state church. Nor did he.
Despite outrageous comments from the pulpit during the acrimonious 1800 election, any fear that the people of New England may have had that they should hide their Bibles in case Jefferson were elected president proved completely baseless. The accusations against Jefferson’s faith in the 1800 election were not true. Disestablishing a state church is not the same thing as opposing a church.
Ironically, today, the secularists, often in Jefferson’s name, are creating a new state religion—a religion of atheism and humanism that has no problem squelching the conscience of believers. Jefferson himself would not agree with that. He once wrote: “On the contrary, we are bound, you, I, and every one, to make common right of freedom of conscience.”
The secularists of today have done a major disservice by twisting Thomas Jefferson’s doctrine of the separation of church and state to mean the separation of God and state. They are trying to remake the U. S. in the image not of its founders, even men like Jefferson (who was not an orthodox Christian), but in the image of the founders of the failed Soviet Union.
Likewise, modern biographers and commentators have misrepresented Jefferson by exaggerating the attacks of clergy against him and ignoring the overwhelming number of favorable relationships. They have fabricated a dominant and simplistic image of anticlericalism that is misleading and false. If any of this is done by those with a political agenda,
we hope the reader will realize that there is no historical accuracy to the view that Jefferson hated the Christian clergy and wanted society purged from their influence.
 Parton, “The Presidential Election of 1800.”