In my urban fantasy, I have several human species that coexist with humans. I'd imagine some like species such as who're classified as Faeries have a stronghold to have intercommunication with humans. But as humans are still humans, they would endanger other species due to fear, hatred, or any other reason. Whether it be Ogres, Giants, Nagas, and more, their numbers are below average compared to other species, and reproduction wouldn't jix the problem.
So if most species made it to modern times, the problem is now about numbers. Let's say they breed in a rate of humans or even slower. What justification would there be a reason to judge an entire species as non-threatened at best and endangered at worst?