Ditto Celerystalkme.

I have flat feet and also have special custom orthotics designed specifically for high impact athletics (running, step, etc). Even when I use them for these activities, I still have foot trouble. In fact, that's the reason I started cycling - for the low impact cardio.

Anyway, I purposely bought high-end super stiff cycling shoes and I use the Ultegra SPD-SL pedals and have had no problems riding distances without orthotics. I did have trouble with my first pair of shoes and SPD pedals after mile 15 or so. The pain would be so bad by mile 35 that I thought I'd never be able to do centuries. Walking after riding was almost impossible, too! Better shoes and different pedals made all the difference in the world (though I changed them both at the same time, so I don't know which one was more beneficial). Oh, and I use only Specialized shoes because they are desgined for people who pronate, which I do. This was under recommendation from my bike fitter who also happens to be a foot/leg alignment expert/specialist (I forget the proper term!).