These allegations were addressed by Jefferson during his life time. Unfortunately for Jefferson he had to be away from his beloved Monticello for years at a time in the service of his country. During this time away from his large estate he allowed his brother and uncle to manage his affairs there.
It was well known by his contemporaries that his brother was having sex with more than one of Thomas Jeffersons slaves. Thomas Jefferson admonished his brother on more than one occasion. Thomas rebuked Randolph in writing for this nastiness.
It is most unfortunate that today the reputation of perhaps one of the very greatest Americans to have ever lived would have his reputation sullied by irresponsible do gooders.
Yes, there is DNA from Jefferson’s family in Sally Hemmings but it is not from Thomas, it is from Randolph.
Before the DNA results it was widely thought that one of Jefferson's nephews (two brothers named Carr) was the father of Sally's children. Apparently the DNA study suggested that at least one of her children had Carr DNA, but the study still tried to argue that all of her children were fathered by Thomas Jefferson.
I have seen the 1870 census record which has Madison Hemings (living in Ohio). The census taker wrote in the margin: "This man is the son of Thomas Jefferson." So Madison Hemings was already claiming to be Jefferson's son then. Did he know? Did his mother tell him that and was she telling the truth? Or did that sound more impressive than saying "I'm the son of Jefferson's brother"?
According to the records at Monticello, Randolph only visited Monticello on four occasions during Thomas Jefferson’s life time. None of the times, that Randolph visited, correspond to a time when Hemming would have became pregnant. However, Thomas Jefferson was at Monticello at the times that she would have became pregnant. That does not, in and of itself, show that TJ as the father, rather it shows that Randolph is probably not the father.