It's easy to view Joel's motivations in saving Ellie at the end as pretty selfish, but if you asked any reasonable human being to sacrifice someone they cared about for the chance they could save the entire world, I doubt many of them would be happy to go ahead with it. And looking at it from Joel's point of view, he's already lost his daughter- he didn't want to go through all that again, even though he spent the first half of the game trying desperaetly not to have any connection with anyone.

And besides, on your journey you encounter Hunters, Cannibals and more- is that really worth saving now? The Fireflies had spent so long chasing their tails in trying to create a vaccine it was all they had- their reason for 'surviving' as Joel talks about. So they came across the best chance they had in so long, so they were just going to go ahead and kill Ellie anyway- damn the consequences. And in retaliation Joel pretty much took away their reason for surviving. 

And right at the very end- when Joel lies to Ellie's face- I'm pretty confident by her reaction that she doesn't believe him at all, but she accepts that this is a shitty world and that he's all she has left, so goes along with it. 

But that's what I like about this game's world- things aren't black and white anymore. 

No, you don't HAVE to throw the bottles, but the help a lot in distracting enemies and splititng them up so you can pick them off- and really useful against Clickers- throw one, draw several into one spot, then a quick molotov to wipe them out all at once. 

And also because I like to finish off the last guy with a shotgun by tossing a bottle into his face then running up to finish him with a melee swing. Feels so satisfying.