Executive summary: Thomas Thorowgood was a friend of John Dury, a preacher and major intellectual influence during the time of the English Civil War and Cromwell's protectorate in the mid 1600's. A whole group of such new intellectuals with various connections to Rosicrucians, alchemists, Jews, etc. poured into England from continental Europe during this time. I am not sure what to make of this passage but Thorowgood almost seems to imply a connection between the dispersion of peoples at the Tower of Babel and the end of the Trojan nation, a subject which appears to have become a very "hot topic" certainly by Isaac Newton's time.
[T]hat Geographia Sacra is an exact and accurate worke, in respect of the subject and materials, the scattering of Nations at the building of Babel, and it may puzzle some mens thoughts, that hee should know so well the places of their dispersion so long since, and yet wee continue ignorant what is become of Gods owne first people, which shall be recovered to him againe, and have not been missing so many yeeres. The Trojans, though now no Nation, live yet in the ambitious desire of other people, clayming from them their descent: The Jewes, once the Lords owne peculiar people, are now the scomme and scorne of the world; Florus calls their glory the Temple, Impiae gentis arcanum; Democritus another Historian said they worshipped an Asses head, every third yeere sacrificed a man, &c. Others speake spightfull things of them, and their pettigree; only the Lacedemonian King, in that Letter whereof you have a copy, 1 Macab. 12. 20. &c. tells Onias the High Priest. It is found in writing that the Spartans and Jewes are Brethren, and come out of the generation of Abraham. The originall indeed of the Jewes is assuredly knowne to themselves and all Christians; Wee have no such evidence for any other people that have now a being; there is nothing more in the darke to the inhabitants of the severall parts of this earth, then their owne beginnings, and tis thus in Countries of along time knowne to each other, and yet in such disquisition they cannot affoord one another almost any light or help; no wonder therefore that the Originall of the Americans is in such uncertaine obscurity, for their very name hath not been heard of much more than one hundred and fifty yeares, tis a wonder rather that so great a part of the world should be till then Terra incognita, notwithstanding the ambition, curiosity, and avarice of mankind carried him into a greedy inquisition after all places and corners where men and beasts abode, or any commodity was to be found [...]
This volume is generally a lot of speculation as to the identity of the natives in America, but the wording and proximity of certain ideas and sentences in the paragraph above seems to suggest more than the author is saying outright. The Tower of Babel is mentioned, as well as God's "first" people (not named, but presumably separate from the Jews who are later described as the offspring of Abraham), and immediately after this, the Trojans are mentioned. It is tempting to draw the conclusion that Thorowgood was implying that the Trojans were the dispersed people who were then of no nation, but living on through other nations that claimed descent from them. Thorowgood does not explicitly say this however and his wording may have just been haphazard in this way. The contrast between the Trojans and Jews is clear however, as contemporary nations sought the prestige of the former while reviling the latter.
The entire text along with the frontispieces of two separate editions are available at this link.