It all has to do with what you put on them. Wearing improper running shoes is probably the most common cause of general foot pain and arch fatigue or even the dreaded plantar fasciitis. You should be fit at shoe store that specializes in running shoes, my favorite is The Runner's Soul.
If you have been properly fitted, know you are in the right shoe, and are replacing them regularly. Then the answer is usually support. Your foot is having abnormal motion that is putting stress on the joints, ligaments and tendons. Sometimes you can use a quality over the counter insert....DON'T go buy them at Walmart or OSCO, you are wasting your time and money. Other runners may need a custom orthotic to control this motion. Only a qualified sports medicine podiatrist can tell you this.
At our practice both doctors are runners and wear orthotics. We will be happy to see you and help decide what is the best course of treatment for you.