In regards to Joel becoming an "antagonist", I think the reason people may see him in this light stems from the fact the Joel is a realist and most people playing the game are idealists. Most people playing the game like to believe in the goodness of human nature, and think that if a cure was manufactured everything would be rooty-tooty and humanity would be saved. Even though saving Ellie was Joels primary reason for denying humanity a cure, having seen the animals humans can become post-apocalypse, he could see what would probably happen in actuality. Once having the cure, the Fireflies would leverage it for power. They would get the government to give them power or have the remaining citizens rebel for the government denying them a vaccine. The marauding bands roaming the country side would be impossible to reason with, most likely resorting to stealing vaccines from fireflies. Due to the Fireflies limited size and the state of Global destruction it would be incredibly hard to spread the cure out of North America at most. Fabricating a cure wouldnt solve most of the problems people have to deal with. Even taking Zombies out of the equation entirely, humans would still be fighting to the death over food and power. A vaccine is only another thing to fight over. So no, I dont believe Joel saved Ellie because he was selfish, but because he saw that at that stage, Humanity was no longer worth saving.