In Star Trek Beyond, Krall monologues to Captain Kirk on how the unity of the Federation is not a strength, but is instead a weakness. Captain Kirk musters a response something like this, "I think you are underestimating humanity." But, was Krall even talking about humanity? Or, was he talking about the peaceful, melting pot of the Federation? Was Captain Kirk referring to something else?
The word "humanity" - however derived from the word "human" - is a property not only of humans, but of other intelligent species, such as those in the Federation. It's a concept which was named "humanity" by humans in the time when humans knew only of humans as an intelligent species. Somewhen someone may find a word which is more descriptive, or we can extend the meaning of "human", like the meaning of the word "man" was extended from "adult male" to "person" in many languages.
I took the statement to only mean the human species, on purpose. Krall's biggest point is that he wants humans (as a race) to endure strife in order to grow (what doesn't kill you ...). He believes that the human race has lost its teeth by joining/founding the Federation of Planets and that's why he wants to bring pain and suffering to a Federation Starbase.
In the final mano-a-mano battle, Kirk - a human - proves he still has a fighting spirit, despite being raised in the warm, safe, cozy environment provided by the Federation. He effectively disproves Krall's point, hence his statement.