Suppose a bunch of Nazis started frequenting Hacker News and dominated every thread with a discussion of Nazism. The site would pretty quickly become known as "that Nazi place" and everyone who's not a Nazi wouldn't want to go there, even if the people running the site don't share the opinions of the people using it.
It's not entirely rational, but if GoDaddy got a reputation as "web hosting for Nazis" that would severely limit their market and hurt their business, so of course they're going to jettison that customer in order to keep all the others.