Dave,
I checked another source on Freeman family information to see if anything "clicked". Merrill Hill Mosher's book, John Freeman of Norfolk County, Virginia contains information about a number of individuals with the Freeman surname. My Freeman line [AARON FREEMAN/MARY BENTLEY] has a chapter, and there are several other lines in the book that Mosher says may or may not be connected to one another.
I noticed that the information posted by an Ancestry.com public member tree reported "Alsey Freeman" as the father of your Thomas Freeman. It's an unusual name - and it pops up in my line, too - as a female name, though.
On page 174 of this book, the children of John and Martha (Linn/Lynn) Freeman were listed in the order of their mention in John Freeman's will [ACCORDING TO MOSHER, DATED SEPT 13, 1797 IN WAKE CO., NC]. "Alsey" was the second of twelve children mentioned in the will. Mosher's book didn't trace the descendants of this Alsey Freeman, but the 1820 census [ACCORDING TO MOSHER, HOUSEHOLD HEADED BY "A. FREEMAN" ENUMERATED IN PENDLETON DISTRICT, SC] reported several children in the household.
Mosher wrote that Alsey Freeman's father, John Freeman, was in what became of Wake Co., NC by 1760. According to Mosher, this John Freeman served as a chain bearer to surveyor Charles Young in Johnston County, a "parent" county of Wake. Mosher also reported that this John Freeman was one of two men with that name in Wake Co., NC in the 1790 census.
I wonder if John and Martha Freeman and their son, Alsey Freeman, will turn out to be your ancestors. Food for thought...
Jean