I always reply to feedback left on my stories, especially when they're left within a week of the story being posted. I tend to neglect responding to comments left on stories I posted months ago, which is not an excuse but more a case of forgetfulness.

As a reader, I'm also far, far worse at leaving feedback for older stories than more recent ones. I think that's definitely a two way street for everyone.

I have a hard time responding to every comment on a non-fic post too. Probably the same way I have a hard time responding to every post that comes up on my friendslist. We're always going to be better at replying to a comment when we feel like we have something to add to the discussion. With feedback though, it seems a little more cut and dry. As you said, I think it does come down to politeness; most people respond to compliments by saying thank you, if they don't–and there's no obvious reason why they didn't–I can't help but assume that they're, for whatever reason, not interested in being complimented.