The idea is that comments are for interesting and insightful discussion about the link/topic. From the guidelines:
"Please don't submit comments complaining that a submission is inappropriate
for the site. If you think something is spam or offtopic, flag it by going to
its page and clicking on the "flag" link. (Not all users will see this; there
is a karma threshold.) If you flag something, please don't also comment that
you did."
http://ycombinator.com/newsguidelines.html