I have REALLY flat feet! So I can sympathize. I used to jog in high school and had to cut it out because it was too hard on my knees with the weight distribution being all wrong due to my feet.

I teach college and notice my feet hurt if I stand on them longer than 20-30 minutes. I do have custom made inserts (they took a while to get used to-don't give up!) and they help-but dumping my extra 40 pounds has helped tremendously.

I usually try to keep my cardio stuff low impact because of it-I do the eliptical runner which is easier on my knees and feet and I do low impact aerobic stuff.