I think, in reality, you are actually paying less. The yarn manufacturer knows you are already paying a premium for premium yarn. They would have to raise the price of the already expensive yarn, if they were to wind it into a ball for you.
Also, I would assume that smaller yarn manufacturers can't afford the machines it takes to wind the yarn into balls.
Your LYS will generally, unless they are really busy, wind your hanks into balls at no charge.
You are comparing apples to oranges. They are not jacking up the price for the same product. You are paying more for a higher quality product. You are also supporting small business, which is sooo very important these days where everything is ultra-corporatized.
If you don't support small businesses, eventually we will all be knitting every project with Red Heart and eating all our meals at Ihop. Or worse yet standing in line all day with your ration cards to buy a few squares of Soylent Green.