It could be the way that you are holding your food on the accelerator. Try using the cruise control more if that is your problem. You have to make sure that you are in a comfortable position when you are going to be sitting in the same position for a while. Also if you have flat feet they may hurt for the same reason.
Sometimes wearing "driving" shoes may help. They are like moccasins that have small nubby things on the sole and heel. It helps, and wearing them when you drive is better for your good shoes -- that get scuffed up when you drive!
If the above ideas still don't help, you could have plantar fasciitis. If you suspect this, you can try to care for it by icing the bottom of your foot & stretching it. You might also need to see a podiatrist for more help.