How big a problem this is might depend on what kind of pain you're having. It is the overall aching of overuse or do you have pain in a specific part of your foot? If it's overall, more supportive shoes and increasing foot strength may help. If it's in a specific place, I'd recommend seeing a podiatrist or orthopedic doctor. If you are injuring a specific part of your foot, you don't want to neglect the problem untiil it gets worse (I know from experience!).
The best exercise I've found for foot strength is slow toe raises--raise up slowly on your toes for a slow count of 8, hold for 8, lower for 8. I did regualr up-down-up-down toe raises forever without much effect, but doing it slowly with a hold at the top has made a big difference.