A nit: There's a subtle distinction between an individual human and the power of human organization and civilization that is implied by the article, but never outright stated.
One-for-one, there are many creatures that are individually more dangerous to humans, and a decent number of people are killed by such animals every year. Indeed, a naked human in the wild is going to be quite fragile and easy to kill until they can bring some technology to bear. But there are no animals or even set of animals that could conceivably wipe out all of humanity at any of our technological peaks from the last 100,000 years. Even the number one killer of humans, the mosquito, is gradually being defeated, going from a vector for disease to just an annoyance, just like the flea.
A lot of rugged individualists seem to neglect talking about the human super organism. That the vast majority of our strength comes from sharing knowledge, making tools, and working together.
And on that same note it should be mentioned that exchange of information between humans is relatively slow and guarded. A group of entities that could exchange knowledge quickly and efficiently would represent an extreme challenge for us.
One-for-one, there are many creatures that are individually more dangerous to humans, and a decent number of people are killed by such animals every year. Indeed, a naked human in the wild is going to be quite fragile and easy to kill until they can bring some technology to bear. But there are no animals or even set of animals that could conceivably wipe out all of humanity at any of our technological peaks from the last 100,000 years. Even the number one killer of humans, the mosquito, is gradually being defeated, going from a vector for disease to just an annoyance, just like the flea.