What kind of punctures are you getting?
I haven't used anything but puncture protected tyres for years now when riding on the road. As you pondered yourself, maybe you could do with a switch to tyres intended more towards road use.
For example I think my brother uses these for his commuter bike. I don't remember him complaining about punctures much
http://www.schwalbetires.com/bike_ti...big_apple_plus