No, that refers to the fact that there is less racism and sexism, and transphobia at this moment in America, and in particular in our institutions than there has ever been anywhere on Earth.
Sam Harris wants to point out that it is not good to ignore this achievement.
That here is a pronoun and Cambridge says:
We also use that to refer back to a whole clause:
A: We’re having a few friends round for dinner. Would you like to
B: That sounds lovely. (that = the fact that you're inviting me)
Why don’t you come at around 8? That’ll give me time to get ready. (that = your coming at around 8)
A: Can you tell Kat to hurry up? We’ve got to leave at 11.
B: I’ve already told her that. (that = to hurry up)
I have put between parentheses what that refers back to.