There's a very large difference between a "good" pedicure and a "bad" pedicure. Unfortunately, the bad pedicurists of the world have given the whole profession a poor reputation. For the record, there are some very good, clean, and conscientious pedicurists out there, and if you have one you trust and you don't have other medical issues, by all means continue to get pedicures. Just be aware of their process and cleaning habits. Some things to consider:
Soaking: If they want to soak your feet in a foot bath before they start, ask how often and how they clean their tubs. Be aware that soaking saps the natural oils out of your feet and can chap them if done for too long or too often, so make sure you restore the moisture balance by putting a good lotion on them afterward. Always dry between your toes, and no lotion needs to go between them.
Cuticles: They are there for a reason! It's best not to let a pedicurist clip or push these back. Often times, this process hurts, which is a good clue that it shouldn't be done--discomfort and pain are your body's way of telling you not to do something.
Ingrown toenails: Be very careful letting your pedicurist dig into corners to get rid of your ingrown toenails. If they bother you on a regular basis, it's generally just safer having your podiatrist look at them and suggest a permanent solution.
Fungus: We naturally have fungus in our environments, and it's sometimes convenient to blame toenail fungal infections on a pedicure or spa, but that's not always the case. Many people end up with fungal toenails without ever having stepped foot (podiatry pun intended) in a pedicure salon. If the salon has good general cleaning practices, you shouldn't "pick up a fungus" by going there.
That said, going to a podiatrist for your nail care is always the safest option. You know the tools will be well-sterilized, and if they see something amiss, they're able to treat it. This is especially important for diabetics--if you're still seeing a pedicurist, you need to switch your nail care to your podiatrist. Most insurances cover diabetic nail care within the cost of the doctor visit, too (though you should check first--insurance plans can vary).