Foot pain may be caused by many different biomechanical conditions or injuries.
Repeated overstressing of the same structure of the foot may cause stress fractures, tendinitis, plantar fasciitis and acute and chronic osteoarthritis.
Injury to the plantar fascia is a common cause of arch pain. The plantar fascia is a tough fibrous sheath that extends the length of the bottom of the foot and lends support to the arch.
High and low arches (flat feet) may cause pain because of strain to the feet.
If you have any worries I suggest you have a TOG gaitscan which will show up any dysfunction or overuse in your feet.