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Jefferson was referring primarily to Protestants who both hated and feared Jefferson (especially in the run-up to the 1800 election), like:

Pastor John Mitchell Mason (Presbyterian)
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“Conscience is God’s officer in the human breast, and its rights are defined by his law. The right of conscience to trample on his authority is the right of a rebel, which entitles him to nothing but condign punishment. You are afraid of being unkind to the conscience of an infidel. Dismiss your fears. It is the last grievance of which he will complain. How far do you suppose Mr. Jefferson consulted his conscience when he was vilifying the divine word, and preaching insurrection against God, by preaching the harmlessness of atheism?”
- THE VOICE OF WARNING TO CHRISTIANS, 1800

Reverend William Linn (Dutch Reformed)
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“I shall only mention what passed in conversation between Mr. Jefferson and a gentlemen of distinguished talents and services, no the necessity of religion to government. The gentlemen insisted that some religious faith and institutions of worship, claiming of divine origin, were necessary to the order and peace of society. Mr. Jefferson said that he differed widely from him, ad that ‘he wished to see a government in which no religious opinions were held, and where the security for property and social order reflected entirely upon the force of laws.’ Would not this be a nation of Atheists? Is it not natural, after a free declaration of such a sentiment, to suspect the man himself of Atheism?”
- SERIOUS CONSIDERATIONS ON THE ELECTION OF A PRESIDENT, 1800