Comment by zamalek

My guess: possibly co-evolution. The article subsequently describes the genetics behind things becoming cute - which would have been completely benign to our ancestors (the core of your question). However, those of our ancestors who completed domestication of these animals (by random chance) would have enjoyed more protection from predators, rodents, etc. Those of our ancestors who attempted to domesticate things without the mutations might have had bad companions at best, and would have been predated at worst. This would have provided evolutionary pressure to adopt animals that were showing early signs of domestication. What we call "cute" is merely "likely to cooperate with us."