One of her six children did have a male Jefferson in his ancestry, but the time does not line up with Thomas Jefferson. The consensus is that the father was probably his brother Randolph (and hence the "uncle" of Jefferson's daughters), but there are at least three other male Jefferson candidates other than Thomas who were present around the time of conception.
That was the only child whose descendants they tested, so it's not established that the children had different fathers. The test indicated that Eston Hemings's descendants had a common ancestry with descendants of the Jefferson family.
The Carr brothers, who I believe where Jefferson's nephews, were excluded by the test, so suspicion fell on Jefferson's brother Randolph, who hadn't even been mentioned earlier, but Randolph wasn't at Monticello during the time periods when the children were conceived.
There were other Jeffersons living in that part of Virginia, but so far Jefferson is still the most likely suspect. Nothing I've seen indicated that he's been excluded as the father.
If you want something to be indignant about, how about the posthumous smearing of the Carrs to preserve Jefferson's reputation?
Most recent item out: The Jefferson-Hemings Controversy
And I'm not particularly indignant, other than at the cynics in the Clinton administration seizing on and publicizing what was formerly a footnote in history to defend the indefensible.