I would guess that the majority of HN users never even think about the fact that the site is affiliated with Y Combinator and its associated personalities.
Quite likely, but also something users that have been around a long time might not think about. From my understanding, in the early days of HN the link was a lot closer (content-wise, pg participating on the site, ...)
I'm well aware of the start up incubator link, but you're definitely right otherwise in my case. When you get here it just looks like a nice lil' news site!