How can I stop foot pain in arch of foot when riding flat pedals?

There's a good chance your flat pedals are too small. To combat arch pain when bike riding with flat platform pedals, I'd recommend the following:
1) Get a pair of Five Ten Freerider shoes. or the stiffer soled Five Ten Impact VXI shoes.

2) Take the insole out of the 510 shoes and replace them with a Sole Softec Response Insoles.  If you have high arches, you will need arch support, which Sole Insoles do an absolutely great job at supporting your arches and your feet.  They are more comfortable than the regular shoe insoles and will make a huge difference in keeping your feet feeling better and more stable while cranking down on the pedals while standing up to pedal or sitting down to pedal.

3) If you have small pedals or large feet, get larger platform pedals. Check out either the Crank Brothers Stamp (Large) Pedals, VP Harrier Pedals, the Catalyst Pedal from Pedal Innovations or the Easton Flatboy Pedal.