It seems to me that the writer is talking to people who are new to jogging, people who have never jogged before. Now, if you haven't jogged, and you start, then your muscles are going to be rather sore the next day. The reason being, you probably haven't used those muscles in that way for many years; i.e., in years, or possibly never used the muscles in that way until now, i.e., maybe (n)ever, and so your muscles are going to be sore, rather sore, and need a day of rest to recover.
