It's a divisive political topic, and he associated an individual post made on an internal Ycombinator forum with Ycombinator itself. Comments of individuals don't represent the company, and by framing it like he did, he publicly dragged Ycombinator right into the middle of a contentious political debate.
That's like saying students at a university don't represent the university, and yet they do and don't, both in the eyes of the people and the institution. It's difficult to say how attribution will be finally concluded in society, no?
In this case the relationship between member and institution is even tighter, and the desperation of sink or swim is more palpable.
All I've been hearing on HN for the last 6 years is how so many things are inherently political, that to not act is to condone, and that organizations should be made to take a stand by their employees/students/passers-by. Why does YC get an exception?