I think Alzrius has hit the nail on the head...
That said, I wanted to start my current campaign with NPC levels as an interesting roleplaying device, but I didn't want my players to feel like they were being robbed a useful level for it. So at 300 XP I had them swap the NPC level for a PC level. It was cool because the campaign started with a period of non-violent encounters. The first was an underwater rescue. It used combat rules, but the danger was drowning, not getting stabbed. And on PC nearly died, and he has roleplayed a fear of water ever since. And that was kind of the point I was going for. So while I know that NPC classes are called "NPC" for a reason, it can be fun to bend the rules occasionally.
But in other situations, I'll stick with the explanation that some things you're just born with. And that can be money for the merchant's son, or street smarts for the criminal's son. The exceptional get class levels. Training and experience can come into play, but the quality of opportunity would be a significant factor, so the more NPC levels you have, the less likely you are to ever have the opportunity to gain PC levels, unless you're exceptionally determined. The captain who rose from low birth might have 3 Warrior levels before gaining Fighter levels. He's had to work harder than those who were trained from birth, which is reflected in the fact that he's got to have more character levels to reach equivalent power to his well-bred peers. It adds color.