Oh, Joel's decision in the end was certainly selfish. you can't take one man's relationship with one girl and call it of equal importance to the future of the entire species. Now, whether that selfishness is repulsive or not, that's more where the question lies, I think.
Personally, I enjoyed Joel. It's rare to see a game take on the amoral protagonist without doing it as either a parody of a villain or an excessively dark, sith-type character, and I found the realism in his portrayal rather refreshing. Honestly, cannibalism aside, there was nothing separating Joel from the enemies in the game, except player perspective.
Soldiers maintaining order in quarantine zones by cracking down on people trying to leave it? Perfectly reasonable, probably more noble, even, than Joel or Tess, though we don't see enough of the governance of the quarantine zones to be sure.
Brigands who scam and rob/murder passersby? Joel did plenty of this himself, by his own admission.
In the end we can fight with Joel because we know what he's fighting for, which is fun, provided you don't ask too many questions about who it is you're killing, what they're fighting for, or why. I admit, during the last area of the game, where I was helping Joel sneak and slaughter his way through a small army of people who were probably the most sincerely altruistic group in the game, certainly more farsighted than he was, and it gave me a sense of guilt I hadn't gotten while gaming since "Spec Ops: The Line"
Still, I don't fault Ellie, and I don't fault Joel. We're only human, and few of us are noble enough to say we could continue to care about the well-being of a world that is now devoid of anyone we care about.
That said, there is ONE thing about the ending that ticks me off: the entire thing about cutting Ellie's head open. hogwash. Fungal infections aren't far divorced from viral infections. Immunity comes from benign strain infections, and inoculations based on them can be created without such an invasive process. Hell, a vial of ellie's blood could probably be cultured and administered to people, giving them her benign-strain infection, and likewise giving them her immunity.
I'm not necessarily complaining about a videogame not being medically accurate, but even a layman knows the story of smallpox and cowpox. it just came off as a cheap device to create conflict.