Seasure I think it was more the whole scenario that unfolded around Angela/Charlotte - Janine claiming Warren Putnam had said he loved her, she ran away with the baby etc
After all that Naomi had to deal with an unfaithful husband - I know they all are by our understanding, but specifically sex outside of the ceremony - and unfaithful emotionally as well as physically. He created that child with Janine in love, the thing he couldn't or didn't do with her.
The censure that followed where he lost his hand and they could easily have lost their position or been executed. And after all that she has to stay with the fucker and accept his lovechild, not their Handmaid-child.
I'm not keen on Naomi at all, I think she's an unpleasant woman, but I also think her antipathy is understandable and I would imagine she's been terrified. Of losing her husband, her life and 'her' child. Maybe she hasn't allowed herself to love Angela because it's all so tenuous and balanced, no one is safe.
And FWIW, I think she does care something for Angela, she allowed Janine in ostensibly as a favour for Janine, but I think also as a last attempt at something for Angela. If she was all butch she would t have done that.
And there's that more than two dimensional character building again! She not just a cipher for a bitter bitch, she's as deep and complex as any of them...