Hi there,
I had the same problem with my son when he was trying to roll. He would roll onto his tummy, and then get upset. This made his naps a mess. They were getting shorter and shorter (his were down to 30 minutes) and he was so frustrated, upset, sore, etc when it was time for a nap, that he couldn't calm down and rest.
One day I finally decided that he was going to have to learn how to roll. We practiced, practiced, practiced. I showed him how to do it on the floor, in his crib, everywhere I could. Within a few days he finally he got it and did it on his own. After that it didn't take too long (a day or two) until naps/sleep got back to normal.
My son isn't a good napper either, and when it comes to developmental milestones, he really struggles with naps. He's 8.5 months now and is trying to crawl, so we're battling short naps again.
Hang in there! He'll get it, you'll be so proud, and think he's a genius!!
Cindy