Coffee is decaffeinated while the beans are "green", prior to roasting, and is an extremely sophisticated process that is only performed at a handful of locations around the world.
Mass-produced decaffeinated coffee typically uses beans that are deemed unfit for regular coffee, apparently assuming that decaf drinkers won't mind. A select few decaffeinaters take a different approach - using high-quality beans that can survive the decaffeinating process with their flavor intact.
There are many different processes which can remove the caffeine from coffee, but they all can be categorized as "direct" or "indirect" methods. We only roast beans that are "water-processed", an indirect method that ensures that no chemicals touch the beans. The direct processes are cheaper, but they require harsh chemicals to contact the beans, which is not only unnatural, but removes flavor.