Primarily, Linn criticized Jefferson because he thought he was an Atheist or was at the very least a Deist whose views directly contradicted scripture. As he wrote in the introduction the pamphlet, "my objection to his being promoted to the Presidency is founded singly upon his disbelief of the Holy Scriptures...and open promotion of Deism." All of his attacks on Jefferson, including those regarding "Indians" and "Negroes" were thus, essentially, attacks on his religious views.

Jefferson and Linn had an existing correspondence discussing their shared interest in studying Native American languages in 1797-1798, and while the letters themselves are devoid of strife it is clear from the pamphlet (Serious considerations on the election of a president: addressed to the citizens of the United States) that Linn takes exception with Jefferson's thoughts in his Notes on the State of Virginia.

In particular Linn cites the following passage from Query 11:

"But imperfect as is our knowledge of the tongues spoken in America, it suffices to discover the following remarkable fact. Arranging them under the radical ones to which they may be palpably traced, and doing the same by those of the red men of Asia, there will be found probably twenty in America, for one in Asia, of those radical languages, so called because, if they were ever the same they have lost all resemblance to one another. A seperation into dialects may be the work of a few ages only, but for two dialects to recede from one another till they have lost all vestiges of their common origin, must require an immense course of time; perhaps not less than many people give to the age of the earth. A greater number of those radical changes of language having taken place among the red men of America proves them of greater antiquity than those of Asia."

Linn argues that Jefferson's claims here are "repugnant to sacred history" because it implies that the Indians are "a distinct race of men originally created and placed in America contrary to the sacred history that all mankind have descended from a single pair [Adam and Eve]" and questions the age of the earth using a non-biblical authority. Put simply, Linn thought Jefferson's explanation for the diversity of Native languages was an implicit rejection of the biblical account of creation and natural history.

Similarly, Linn complains about Jefferson's infamous Query 14, particularly his claim that "the blacks, whether originally a distinct race, or made distinct by time and circumstances, are inferior to the whites in the endowments both of body and mind...Will not a lover of nature history then...excuse an effort to keep those in the department of man as distinct as nature has formed them?"

Once again, Linn asserts that "would a man who believes in a divine revelation even hint a suspicion of this kind?" and even calls Jefferson a "true infidel." Finally, he puts it more directly insisting that Jefferson has "degraded the blacks from the rank which God hath given them in the scale of being! You have advanced the strongest argument for their state of slavery! You have insulted human nature!...we exclude you, in your present belief, from any department among Christians!"

I hope this helps!

Related Sources:

“To Thomas Jefferson from William Linn, 25 May 1797,” Founders Online, National Archives, last modified June 13, 2018, http://founders.archives.gov/documents/Jefferson/01-29-02-0314.

“From Thomas Jefferson to William Linn, 5 February 179[8],” Founders Online, National Archives, last modified June 13, 2018, http://founders.archives.gov/documents/Jefferson/01-30-02-0051.

“To Thomas Jefferson from William Linn, 8 February 1798,” Founders Online, National Archives, last modified June 13, 2018, http://founders.archives.gov/documents/Jefferson/01-30-02-0057.

“From Thomas Jefferson to William Linn, 2 April 1798,” Founders Online, National Archives, last modified June 13, 2018, http://founders.archives.gov/documents/Jefferson/01-30-02-0160.

“To Thomas Jefferson from William Linn, 4 April 1798,” Founders Online, National Archives, last modified June 13, 2018, http://founders.archives.gov/documents/Jefferson/01-30-02-0164.

Thomas Jefferson, Notes on the state of Virginia. Philadelphia: Printed for Matthew Carey, 1794. (Available here: https://quod.lib.umich.edu/cgi/t/text/text-idx?c=evans;cc=evans;view=toc;idno=N20681.0001.001)

William Linn, Serious considerations on the election of a president: addressed to the citizens of the United States. New-York: Printed and sold by John Furman, 1800. (Available here: https://catalog.hathitrust.org/Record/000515117).

Fred C. Luebke, "The Origins of Thomas Jefferson's Anti-clericalism," Church History 32 (Sept. 1963): 344-56.

Linda Kerber, Federalists in dissent: imagery and ideology in Jeffersonian America. Ithaca: Cornell University Press, 1970. (pages 55 and 92).