The problem with Patagonia is that organic cotton is not better for the environment. They are just funding groups to fearmonger against conventional farming to scare people into buying their stuff. Their efforts against GMOs has detrimental impacts for the developing world.
Organic is a marketing scam, and Patagonia is just a part of that. It costs more because it has more inputs and less yield. More inputs and less yield in agriculture is bad for the environment.