In the following locations:
- Puerto Natales
- Punta Arenas
- In the lodges, refugios along the hiking trail of Patagonia
Which currency do they accept? It looks like the above locations are within Chile. Do they only accept Chilean pesos?
Yes, in Chile most venues will only accept Chilean pesos.
It's different across the border in Argentina though, there you will fare much better with US dollars.
Update: In December 2015, the new Argentinian government removed the exchange restrictions which fed the demand for black market dollars, so they are now probably in much less demand.