Business is as business does. Sam Altman has stated he is not going to cut ties with Thiel over political issues [1]. At their level of influence, doing so burns bridges unnecessarily, and sends a clear message that polarization and bubble-creating is OK, and its not. YC wants to set a good example for the tech community by influencing the world in a positive way (e.g. ACLU) and not in a negative, spiteful way (dropping Thiel).
http://www.recode.net/2016/10/16/13302120/y-combinator-sam-a...