There are risks inherent in every activity, and for generally healthy clients, the risks associated with a pedicure are very small indeed.  By generally healthy, I am including anyone who's immune system is functioning normally and your Doctor is the best person to help you assess the status of your health.
At Bella Fontana Spa, we help protect your health by using a special foot soak that is anti-bacterial and anti-fungal.  It contains urea, salicylic acid and aloe vera, among other ingredients that cleanse and help soften calluses.  According to the manufacturer, some of the retail products, especially the Anti-Fungal Formula 7, contains 1% Clotrimazole. an anti-fungal agent that relieves itching, scaling, cracking, burning, redness and irritation associated with fungus, including ringworm and athlete's foot and protects the feet from picking it up in the first place.  The moisturizing and anti-fungal formulas use a dermal integration technology, DIT, that allows the product to penetrate easier and faster into the skin.  The mousse mimics the skins own composition closely and contains CoEnzyme Q10 and urea making it the most effective moisturizer available.  Read more about Footlogix.
Recently, SpaBoom put an entry on their blog about Pedicures, and I commented:

Think about the fungal and bacterial load at the gym, department store carpet in the shoe department, and the parasites in the lake or your own front yard. Our first line of defense, as wonderful as many of the smell and feel good products out there, is a specialty anti-bacterial and anti-fungal foot soak. We also use EPA rated anti-bacterial, anti-tuberculoidal and anti-fungal sanitizer in our pipeless pedicure stations. We have an autoclave, disposable tools and more all to keep our clients safe. Unless a client has a compromised immune system, our pedicures are as safe as any other activity. Sure, there are risks like a nick or cut for both the client and the technician. Take care of the customer and reassure them you are using the best products to protect them. Clients, please ask about the sanitation protocols and take good care of your feet everywhere you go!

It is important to me that you feel safe and know that I am doing everything I can to take care of your health and well being.  In my judgment, pedicures are safe in an environment that is conscientious about cleaning their equipment and implements, or uses disposables, and uses products that facilitate protecting and caring for your skin.  There are risks, but the risks under these conditions are typically a nick or cut that can become infected without care, abrasions or infection or other injury that is no greater than what you might expect at your local gym, on the beach, in your backyard or medical office.  Remember, we put our hands on your feet and in those bowls too!