If you are rate limited, a moderator has manually applied a rate limit to your account. Accounts are not rate limited by default. You can appeal the decision by emailing hn@ycombinator.com.
I think there's a short-term rate limit applied to everyone, e.g. you get a message if you try to post three replies in the same minute. I've seen it once, and I don't think I'm active enough to have earned a manual flag.