Protection or selective breeding
People may be less likely to kill off creatures that look very human compared to some that don't. There is a reqal-world precedence for this in "Samurai crabs", a species of crabs with a shell that bears a pattern resembling a human face, which many believed to be the face of an angry samurai. It has been hypothesised that crabs with shells resembling samurai were thrown back to the sea by fishermen out of respect for the Heike warriors, while those not resembling samurai were eaten. Thus, the more closely the crabs resembled a samurai face, the more likely they would be spared and thrown back, causing selection for this sort of look. Similarly, 'faeries' that somewhat resemble humans may have been selected or even bred to more closely resemble humans.
Cuteness may also be a factor. People tend to find squirrels cute and hence refrain from killing them - we even feed them. If squirrels looked like rats, we would not be so kind. Similar forces could have caused selection for cute humanoid faeries.
A fairly big caveat is evolutionary timeframes. Humans haven't existed long enough for evolutionary pressure to produce 'surprisingly humanoid' beings from very different species. Selective breeding is far more likely - just look at how dogs have been bred from wolves to all sorts of sizes and looks.
As for what species may be the root, on Earth insects would be the most likely candidate. It is far more difficult to add limbs or wings through breeding than to remove them. Insects have six legs and four wings, so all we need to do is regress one fair of legs into nothing (or accept fairies with four arms). The thorax (which is where all insect limbs and wings are attached) would have to be expanded and elongated, while the rear body would have to be much reduced, perhaps ending up looking like a sort of short, stubby tail. The bodies would be exoskeletal rather than having soft surfaces. They would have mandibles rather than mouths like ours. Their overall shapes might be made to resemble humans, but all sorts of details would stand out.
Another candidate might be a mammal similar to a bat or flying squirrel, or perhaps some kind of flying monkey built along similar lines - but then, the wings would have to double as arms, and they would be leathery rather than insectile. On the other hand, it will be far easier to breed them to have bodies and faces that are very close to humans.