Stephen Herrero is literally the researcher who wrote the book on bear attacks--it's called "Bear Attacks." He was the source of the NY Times article you linked to. But that article (and the journal article it referenced) was only talking about fatal attacks. The vast majority of fatal attacks are predatory attacks by males. Defensive attacks are much less likely to be fatal, and that would include instances where females defend their young.
Yes, I'm well aware that black bear attacks are quite rare, and the risk for an AT hiker is miniscule. I'm just saying that there have been defensive attacks by females with cubs for black bears.