There are a couple reasons for removing the skins of tomatoes for canning purposes.  First, it reduces the potential bacteria that would end up in the jars, thus reducing the risk for spoilage and contamination.  Secondly, peels have a tendency to get tough and increase the bitterness of the product when canned and would affect the quality of the product.  Lastly, since peeling tomatoes was a widely used practice when recipes were tested, the recommended processing procedures and times are based on using peeled tomatoes and using unpeeled tomatoes has not been evaluated.  Unless a recipe from a reliable source (USDA, Extension or Ball) allows for using unpeeled tomatoes, always make sure to peel them before canning.