Why do the bones in my feet hurt?

Maybe they : Need support. Try an arch support.

Many causes: This could be the joint pain from arthritis/ improper alignment, flat feet, etc - see a foot doctor for a detailed assessment.

NEED FOR CUSHION!: Most shoes aren't always what is bad, usually it's the crummy insoles they come with! there are many possible reasons that you may have painful feet, but try cushioning arch supports like spenco polysorb cross-trainers(http://www.Spenco.Com/products/footcare/poly-sorb). If these don't help, see a podiatrist.... Also try an otc anti-inflammatory, like aleve (naproxen).