We did go out and exterminate (almost) all wolves because, yes, they would kill us while we were out and about. We also do happily gas/poison/fill-with-molten-aluminum entire nests of ants, not because they're killing us, but just because they're eating our food / for fun.

And even when we didn't mean to -- how many species have we pushed to the brink just because we wanted to build cities where they happened to live? What happens when some AI wants to use your groundwater for its cooling system? It wouldn't be personal, but you'd starve to death regardless.