I'm not going to post the whole article here, only the link. There was some argument going on in the Fallout 3 Hate thread about what is and is not a believable motive in Fallout.

The State of Gaming Nature

I simply think this article does a better job of discussing the matter than I could.
In short, WTF, it works this way because the story the authors of Fallout 3 wanted to tell, as is true of many Fallout games, was of civilization (represented by James' Project Purity) vs. the brutish and cruel wild (represented not only by presentation of the wilderness, but also by James' hardships.)

Nice article, I love my philosophy and games. I did a college paper once where I discussed Fallout 3 a bit and--SPOILER--the mission where you can help the ghouls move in to the tenpenny tower, and how even if you do the "right" thing and convince everyone to let them move in, they end up killing everyone when you're away, making it so it would have actually been better to just kill the ghouls with a short-term wrong leading to a long-term positive benefit, a utilitarian viewpoint of the common good.

I like to think even in a world like Fallout there would be people who just want to do the "right" thing as a pre-apocalypse society would define it instead of living by post-apocalypse standards of murdering and doing whatever it takes to survive. Someone out there would want things as a pre-end-of-world way.

UPDATED to indicate a spoiler for Fallout 3.

You're probably true about what the F3 writers wanted to tell, and I don't object to it. As you said yourself, every fallout game is somewhat built around this idea. What I object is the way they decided to picture it: with a holier than the pope white knight kind of guy who's purpose is to Change The World and Make It Better For Everyone (lets hear hallelujah!). That's not believable. That's so bloody cliché, that my teeth hurt when I even think about it.

Eh. To each their own.
I will point out that he's not perfect. He abandoned his child. Perhaps his goals were lofty, but as a father he was sorely lacking.

It saddens me that the concept of someone doing good for the sake of doing good is one met with disbelief.

Not very realistic, as humans are flawed. Also, I've viewed the darker, selfish side of humanity a great deal since about 2009 so I would be a little skeptical myself.

I don't think any of us are disputing that dark and selfish motives abound. Indeed, Fallout would be empty of people if you removed all those with dark or selfish motives.
If you include the craptastic job James does as a father as a deal-breaker, which some reasonably might, it'd be empty of him, too. Just happens it's probably his worst trait.

Also, James abandons his lofty goals in favour of happy married life. Only with the wife dead and life offering only endless monotony under an oppressive regime, he finally decides to do something worthwhile instead.

If it makes it any easier to believe, a success would have brought him eternal fame and glory. Better than slaving away in a bunker, eh?

Ew. He abandoned his child because we went a little nutty after his wife passed on.
Gads. Shades of my father.

James seems to genuinely care for you in the game, he just doesn't care enough to actually stay with you. Then again, if he didn't abandon you we wouldn't really have a game, so I guess his being a bad father kind of helps.
Helps at least in terms of giving us a fun game, not in the sense of your character having a happy life.

I'm certain in The Hobbit Tolkien says something about how nobody likes a happy story.