Look to your feet, shoes and/or insoles. What kind of shoes are you wearing and how do they fit? How stiff is the sole? If you bend the shoe by pushing the front of the shoe against a table does it bend at the ball of the foot or more like half way back? Are your shoes loose and you really have to cinch down the laces, or are they narrow and if you are not standing on them do you get hot spots?
Are your shoes supportive under your arch? Stand with your feet about a foot apart and bend your knees, does your foot roll to the inside like the shoe is sagging inward? This ‘give’ (shoe fitters call it collapse) if too much can be the root of many foot ailments. About 90% of people pronate. It’s normal. It’s when you overpronate for the activity that you are doing that causes problems. The opposite of pronation is suppination also called rigid foot. This foot has high arches and you tend to walk on the blades of the foot. Extreme Pronation results in flat feel though flat feet and pronation can be separate things. In other words you can have flat feet and normal pronation. Pronation is how your foot flexes, part of the shock absorption for the lower limbs.
Do a google search on “pronation” to learn more about normal pronation and excessive pronation. Typically you fix the pronation to where when you flex your knee it tracks straight over the 2nd toe (Next to the big toe)
How do you pedal? Do you pedal on your arch or on the ball of your foot? Which ever it is try the other way and see if it changes anything.
Here is an article on hot feet: http://www.roadbikerider.com/articles.htm#How%20to%20Solve%20Painful%20Hot%20Foot
A simple metatarsal pad might be all you need.
Here are some examples: http://www.footsmart.com/ProductList.aspx?ailmentId=87
Here is an article with some foot exercises/stretches you can do that might help along with any pads or insoles. http://www.trifuel.com/training/strength-training/correcting-overpronation
You may find that some stretching/exercises for your feet is all you need. One of things that I find helps my feet is running which I do by throwing frisbee with a buddy of mine. The stopping and starting, changing directions keeps my feet flexible, where sitting all day and just cycling or walking do not.
Here is some more info about cycling and pronation: http://www.bicyclesource.com/bicycle_overuse_injuries_orthotics
If you feet do collapse, it’s called Pronation and if excessive better insoles will help you. Here is just about the most popular brand: http://www.superfeet.com/
You would use either Blue or Green. Blue is for shoe where there is not much room in the shoe, or where the Green insole is too aggressive of arch support. Both of these are meant to be worn in shoes where you can remove the stock insole. If you can’t remove the insole there is black for that situation.
This should keep you busy and give you a jumping off place to find more info on the net.
I wear superfeet to control another kind of foot pain called Plantar Faciitis (heel pain) I wear Green in my Skate shoes i use for riding my uni and blue in my running/walking shoes. I also use Green in my ski boots.
If you have a New Balance store near you go in and have them size you up. They will demonstrate how much you do or don’t pronate (the opposite of pronation is supination also called rigid foot). They will put you in shoes that correct what pronation you have so you know what that feels like. If you have a good running shoe store (see if you have a ‘Fleet Feet’ near you) could also help you find what proper support feels like. I’m not saying you need new balance shoes, I just want you to feel what being properly supported feels like so you can go for that feeling with insoles.
A good fitter will ask you to stand up and flex your knees, and ever better is to watch you walk away in bare or stocking feet. They should note how your knee tracks when you bend your knees. Beware a sales person who offers you shoes without at least some of the assesment I mention here.
Summing all this up: start with exercise/stretches and a metatarsal pad (at any walgreens, Rite Aid, etc.). If that doesn’t seem to help consider insoles. Superfeet is just one brand (there is also ‘Sole’ and ‘PowerStep’.
You can try on superfeet at an REI store. I like REI because if you are a member its a 100% satisfaction return policy. If after a couple weeks you decide that the superfeet aren’t helping, or causing you other foot problems they can go back. Superfeet are only little more expensive than online. PowerStep on the other hand can be had for much less expensive online than in retail (New Balance stores carry ProStep).
In Prostep the ‘Pinnacle’ is the thicker, more supportive insole and the ‘Original’ is the one for tighter fitting shoes. Where ‘tight’ has more to do with volume of the shoe more so than length or width. In other words how close is the top of your foot to the top of the shoe.