You ask a very good question. You can always write a note on the survey itself giving them more information about what you think and how you feel. You can also send a separate note without identifying yourself. This is perfectly acceptable if you are concerned that a particular health care provider will be offended or hurt in anyway. That way it's not clear who was treated or by whom.
Surveys don't always take into account the difference between service received and effect of service. A patient can be happy with the care received but unhappy with the results. In fact a recent study at the University of Florida looked at this with low back pain patients. They found that patients who had high levels of pain and minimal pain reduction were still happy with the way their pain was managed.
A good patient survey will ask questions to find out both satisfaction with service delivery versus results of services.