If you're new to commuting, it's just that your neck is compensating for all the road vibrations, and not used to doing that. Stretch before and after, if stretching helps you, anyway. It does nothing for me. In my experience, after a few weeks, your muscles will get stronger and more used to working, and the pain will go away. In the mean time, take ibuprofen and use heat or cold to help the muscles relax.

I actually had my first bout with neck pain in a while, because I doubled my usual commute today, and used drop bars for the first time. Bit different load on the neck, that.