Sore hocks are actually pressure sores. Pressure on the hocks rubs off the fur, then the skin. In bad cases, bleeding sores will develop. These sores can go as deep as the bone, infecting the bone, tendons and muscles. Extreme cases lead to amputation and/or death.
So, sore hocks can be serious issues. However, I think you've caught these in the early stages. Do their feet look like this, more or less?
http://s216.photobucket.com/albums/cc43/velvetlop/?action=view¤t=SoreHock.jpg
Some rabbit breeds which are less furry, are prone to sore hocks, such as English Lops and Rex. Wire floors may cause it, but carpet can also cause it. Any hard/abrasive surface can be a culprit. Any rabbit can get them. It's not an absolute sign of neglect, at all. And, some rabbits will have them no matter what you do.
Keep their nails trimmed. Long nails can make them lean back on their hocks putting more pressure on them.
And, keep their weight down. Obesity can cause sore hocks.
Exercise! It keeps the weight down and helps the blood flow through the effected areas.
You can also try fake sheepskin (cheap at Wal-Mart in the dog dept). Pixel never liked it, and would rip it up.
You're doing fine. Just watch for abrasion on their feet. The big worry here is infection.
