In battle against Pain, we have seen Naruto defeating certain Pain paths with a single punch using Sage Mode. Later when he was the Kyuubi overtakes him, he hit several punches and kicks on the Deva path but couldn't defeat him. Why?
Right from the start we can see that Yahiko was the main Pain used by Nagato. This is shown when he destroys the village with a single attack, the ringed black orb jutsu... It draws all other Pain's power making them all faint.
Now, why didn't he just die with one punch? Other than it being a possibility of fillers, as mentioned by someone else... Since all other pains have been destroyed, this would allow Nagato to put all his remaining power within that single Pain, Naruto at that point wouldn't be able to kill Nagato with a single blow.