Lately I have seen more than a few "why is this here?" type comments on topics that have already gone popular on HN. The bottom line is that happens because not everyone has the same interests, and this is a social site with many different people on it.
If the fact that you have to share this wonderful digital playground with the other kids really, really bothers you, then this is for you. It's a Greasemonkey script called "HN Toolkit":
http://userscripts.org/scripts/show/25039
Part of the functionality is the ability to blacklist submissions, either by keyword in the title or in the domain (or entire domains, whichever way you want to look at it). It cycles through the list of stories and matches each against the blacklist, adding style = 'display: none;' to each match found.
Hope this helps.