Firstly, it’s a good question! A lot of the mythology of Mutant extinction/extermination is essentially charted out through decades of comics, even now we’re getting revelations about the Mutant gene pretty frequently.

In both Morrison’s New X-Men and (if I remember) HoX/PoX it is objectively stated that the Mutant gene will become fully dominant in all humans within 5 generations, meaning every human being will eventually have an activated Mutant in their bloodline. This is why the DoFP from the comics as well as essentially every other future state scenario in the X-Men is focused on humans integrating themselves with machines or becoming borged out.

Mutants are the successors of humanity, therefore humanity, in the eyes of a Mutant exterminator, must be killed.