Someone has to envision, construct and distribute the shoes that eventually grace your feet. These factors play a part in the price of your shoes:
Quality workmanship - Handmade products that have a long history of quality workmanship can command top dollar. Italian shoes, anyone? Shoes designed for the wearer's arches that fit like a glove and boast soft leather go for big bucks. When you want fit, function and style, go with quality every time. If your feet are slightly different sizes or your poor, abused toes are giving you trouble, handmade shoes will fit the bill beautifully. They're constructed by artisans and the special service will cost, but oh, the comfort.
Cutting-edge technology - Running shoes, hiking shoes and work boots have the power of science behind them, and all that research adds to the cost. Shoes designed to stay cool, weigh very little or provide mega protection are expensive. Innovation and the time and money it takes to achieve it drives up prices. Without the economies of scale in production to bring them back down again, you pay more.
Limited distribution - It's the law of supply and demand at work. When a particular shoe or shoe manufacturer is hot and supplies are limited, the price goes up. It's the same in nearly every industry and with every type of product. When you just have to have it, you pay for the privilege.