There's a difference between "nice guy" and "Nice Guy". A "Nice Guy" is like Leonard on The Big Bang Theory; whiny, neurotic, too obsessed with thinking "but I'm nice, why won't anyone have sex with me?" to realise that, actually, it's because he's whiny, neurotic, obsessive and generally odious.
Then there are actual nice guys, some of whom do well and some of whom end up left out because they don't want to impose. Yes, a lot of them are lacking in confidence, but I don't see how that makes them horrible people; there's a difference between nervous and clingy, after all.
So it's a much broader spectrum than the "Do girls prefer Nice Guys or Bad Boys?" dichotomy suggests. I tend to consider myself in the "nice guy" category - I've had one girlfriend in my life (now my wife and six months away from being the mother of my first child), and we slipped into the "romantic pairing" thing quite quickly, eschewing the "I'll be your friend so you can learn to be dependent on me and then you will love me" route that "Nice Guys" often take.
So why did I wait twenty-six years before finding a girlfriend? Well, it certainly involved a degree of nervousness, of not daring to ask a girl for fear of rejection - but it didn't involve the stalking, the creeping, the sinister "in time, you will love me..." psycho-villain stuff that is so associated with the Mk I Leonard-class "Nice Guy".
So yeah. That's my take on it.