As your foot hits the ground its primary function is to absorb the impact and then to mould to the ground to give you a stable foothold. As this happens, the arch of your foot flattens and your leg rotates inwards (this is known as pronation).
If you have flat feet, too much rotation can occur resulting in you adopting a 'knock kneed' posture, your legs to rotate inwards, your pelvis tipping forward and your back over arching. This can cause foot, calf, knee, hip and lower back pain, and maybe pain in your upper back or neck.