There are two things to keep in mind: Most of the food you will encounter is coming from a commercial system; and there is not the same level of oversight at the consumer level (restaurants) that we are used to here. There are pros and cons to this.
Chile is a major agricultural producer. Much like the U.S. or European countries like Spain, commercial agriculture is the norm. Bio-engineering, synthetic pesticides, and chemical preservatives are common – just like the grocery stores and restaurants of the western world. The organic movement is faint and local production and sale has not become "cool" yet. It's a bummer that the food visitors eat is chemically raised, but at least we know it is not full of fertilizers of human manure or other things I heard rumors of when I first started traveling here.
Food safety inspections are not nearly as common in restaurants as they are in the U.S. This means some restaurants are cleaner than our homes and some are not so clean. In my experience the most worrisome establishments are those that serve hundreds of people a night and have a limited menu. When the meal preparation looks like an assembly line, things get missed. A little cross contamination and soon dozens of people have poop that looks like fish food. But what about the small, family run restaurants in towns and on city streets? Again, my experience has traditionally been positive. The owner is probably eating the same meal as the patrons. If the guest gets sick, he will never return. I have had great experiences in the smaller establishments.
The take home here is this: don't assume the big, famous, elegant hotel is the safest place to eat. And don't judge the local establishment by the condition of the chairs or floors. Can you see the kitchen or meet the chef? This is probably a good sign. Eating in Chile is safe and can be great. Enjoy!