Vox actually covers this really well https://www.vox.com/2020/6/5/21280425/new-york-times-tom-cot...

Basically it boils down to:

* it was a fairly dangerous opinion with fabrications that weren’t vetted by the editorial team

* it was disrespectful and dangerous to the safety of their employees of color. The safety of people should not be a partisan issue

* it compromised the reporting abilities of other arms of the NYT