Most of the pressure from your pedal stroke is focused through the ball of your foot, and some shoes don't distribute that pressure very well. You likely need some type of insert in your shoe to "spread the load" across your foot better. I had the same issue and finally bought these shoe inserts that you put in the oven and then put in your shoes to conform to your feet. They worked pretty well, but probably were not as good as a custom orthotic. They were also only $30. I have used Spenco inserts to some degree of success as well.

Chad