Very easy to travel independently through Patagonia: you can easely book the hotels and flights trought internet. You have to pick the places (whales watching at Puerto Madryn, continental glaciers at El Calafate, the southest city in the world: Ushuaia, great wines in Mendoza). Don't hesitate in asking further questions around places in Patagonia! And enjoy Patagonia, it's really a great place in the entire world! about 6 years ago
We travelled to Patagonia through company Cocha (cocha.com). From Punta-Arenas we flew by small plane to Porvenir where we were met by a local guide summoned by Cocha. I think this is the best way to travel there.
P.S. And Ushuaia is in Argentina not in Chile. about 6 years ago