There are a few different factors that contribute to the cost of a repair: Cost of materials, cost of tools, cost of time, and cost of training.
Cost of materials and tools:
Because instrument repair is not a common trade, the tools and materials used are not mass produced like the tools used in other trades. For example, there are hundreds of manufacturers of tools and materials for electricians, plumbers, mechanics, etc. But in the instrument repair field, there are only five manufacturers of the specialized tools and supplies repair technicians use. When a product is mass produced and there many manufacturers of that product, the price of that item is relatively low. Instrument repair tools and supplies are not mass produced and there are only a few suppliers of those items. Thus, the price of these tools and supplies are expensive.
Cost of time:
Instrument repairs vary greatly in the time they require to complete. Some repairs, like soldering a loose brace on a trumpet or replacing one cork on a clarinet, are usually simple and might take less than half an hour. Other repairs, like removing lots of dents from a brass instrument or overhauling a saxophone can take a couple of days to do well. Instrument repair, when done properly, is an exacting and time consuming process. This is necessary to ensure a lasting and quality repair.
Cost of training:
To learn the instrument repair trade and be skilled requires many hours of training and hands on experience. There are very few places a person can learn the repair and even fewer places that can produce an excellent repair person. Not that instrument repair is rocket science, but it is not something that can be learned in a month or a year. It takes many years of experience, innate mechanical ability, and fine motor skills to repair instruments well.