Feebas, contrary to popular belief, are not an endangered species. Their population size, although low, has remained more or less steady through recorded history. Once their evolution method was discovered they became prized by trainers and coordinators alike, and the Feebas population today is likely higher than ever before.
What Feebas are is remarkably difficult to catch. Part of this is attributed to their camouflage; their appearance, although unappealing to human aesthetic tastes, shields them from trainers and pokemon alike. Furthermore, unlike nearly all other water pokemon, Feebas have sufficient eyesight to distinguish actual food from a fishing rod's lure under nearly all conditions. Only in the murkiest areas of the Hoenn swamp they call home – areas which change constantly with the angle of the Sun to the Earth and the growth of aquatic plants - can a Feebas be fooled into confronting a trainer. Fishermen from as far as Unova enter Hoenn's swamp in the hopes of catching a Feebas themselves: Wailord may be the pokemon novels are written about fishermen confronting, but the Feebas are actually a much greater challenge. Those who seek to train one often attempt to catch one in the wild, but rarely do they succeed; unless they are astonishingly lucky, they will give up, save up their money, and buy one from a breeder.
Interestingly, despite their skill at avoiding capture, Feebas are not particularly difficult pokemon to tame. Perhaps the difficulty of finding them is a test to prove their trainer's worth, or perhaps once they leave the one swamp in Hoenn where they can be found, they have nowhere to go but back into their pokeball.