Whenever you push yourself to do more than your muscles are used to, you're going to get some aches. If you settle into a routine with no further increases in pace or mileage, then the aches will probably stop - but I think you'd get bored. It does get better, however.
Self-massage, either with you hands and some baby oil, or a foam roller or "The Stick" or something, can be useful to help with sore muscles.
Edited: 21/10/2012 at 20:49