There will be spoilers
I can certainly recognize Joel's motivations for saving Ellie, and I can empathize with it. Not being a parent it is difficult know if I would make the same choice, but I'd like to think that I would. With that being said, I find it difficult to really believe that Joel is a good person. Aside from putting Ellie before humanity (more on that in a bit), he, without hesitation tortured a man, killed him and then killed another in cold blood, to get information. Unlike elsewhere throughout the game, he wasn't in immediate danger at this point. Neither men were a threat to him and yet he murdered them both to get whet he wanted.
His massacre of the Fire Flies brings up a whole new can of worms though. At this point it is clear that he Ellie is his surrogate daughter and that he is out to rescue her from being sacrificed for the mere possibility that it will lead to a cure/vaccine. I'm not convinced though that he really did it for her sake. When his daughter was shot at the beginning He had the rather curious reaction of saying, "Don't do this to me," making it seem like his first concern was not so much that her life was being taken from her, but that she was being taken away from him. Though the first two seasons of the game Joel demonstrates an aloofness or detachment toward others that I believe is in an effort to not have to go through the loss of any one he truly cares about, like he did with his daughter.
The dynamic between he and Tess is another bit that lends to Joel's general detachment. In an effort to keep his life as simple as possible he has hooked up with an alpha personality. There are hints of a relationship between them but it always felt like mutually beneficial arrangement where they can depend on each other and their ability to survive, but there never seems to be any emotional attachment. She is clearly the one in charge and because she calls the shots, he can afford to not become too invested in the outcome of their activities. When she tells him that she was bitten, there is a moment of disbelief that suggests that he is contemplating being the one who has to make the decisions from now on and for a time he seems like he isn't quite sure what he should or could do.
You can see that Joel starts to see that there is a possibility of Ellie being some one who could fill Tess's shoes as some one to rely on for survival after he has her cover him with sniper fire, after the hotel. At this point he trusts her enough to give her a weapon, but her well being beyond the task at hand never seems to enter his mind until she brings up her desire for him not to die, at the plantation. At that instant, he lashes out to reestablish the boundaries between them, but this is undoubtedly the major turning point in their relationship, and also the first time Joel has had an emotional attachment to anyone since his daughter.
This emotional attachment is what I believe ultimately drives him off the deep end. He is faced with the prospect of losing her when they are separated for the first time after they have built their new dynamic, and he is driven to torture and murder to get her back. I believe his motivation to save her is out of self preservation and not wanting to go through losing another daughter, not so much that he wants her to life a full life or even for the good of human kind. It all comes to a head when he is faced with her sacrifice and he becomes completely unhinged and decimates the Fire Flies, kills who is possibly the last surgeon on the planet, and takes away the only lead on a possible salvation for humanity.
It feels a little like splitting hairs debating whether his motivation for saving some one he loves was for the altruistic or selfish purposes as it is certainly two sides of the same coin, but it is a subtle difference between a character who I can identify with or a character who I wish I could identify with. Or maybe it's the other way around.