It will take more than the right boots to keep your feet feeling good. Socks with padding around the toes and balls of your feet will let you ride in comfort. Mid-calf length socks work well with boots. Be sure they're made of wicking material to prevent your feet from sweating.
You'll want some foot protection on the outside of your boots, too, especially if your ride takes you through the rain or snow. Overshoes are made of specially treated nylon for waterproof protection. They slide over your shoes or boots to keep them dry and looking good. Your socks, feet and pant legs will also stay out of the elements. The lugged soles are much like hiking boots to provide the traction you need when you dismount. Insulated and non-insulated styles are available.