The Darwinian 'Survival of the Fittest' doesn't mean the most powerful, more the most suitable.
Being the giraffe with the longest neck isn't an advantage unless it lets you breed and pass on your genes better or more successfully. If all your energy has gone into growing a neck, you'll be outbred by your cousin with the most suitable length neck, and enough energy left over to sire short-neck giraffes.
Apocalypse may just regard 'The Strong will have Dominion over the Weak' as the same thing. I don't know if he read much on genetic evolutionary theory (That's more a Mr Sinister thing, right?) Or rather the writer did.
His is a somewhat flawed philosophy in a world of mind-control and psychic dominance, but from a barbaric 'strong loners punching each other' comic-book world it seems suitable.
While he considers himself to be the father of mutants, their progenitor and Ur-Mutant, he would have to respect the pure martial power and abilities of the universe's powerful non-mutants - Spiderman, Thor, Loki, Captain America, Black Widow etc.
I don't think that this would extend to Tony Stark and Antman though. Their reliance on technology and tools is anathema to his Nietzschean 'Will to Power' - otherwise you'd have to consider the builders of nuclear weapons to be as powerful as mutants.
In the classic 'Mutants as minorities' parable Apocalypse is more than Professor X's Dr King, or Magneto's Malcolm X but as a superpowerful Mutant supremacist - like how a KKK member might imagine a vengeful black Superman.
(Obviously a massive simplification of civil rights, racial politics and comics - not a can of worms I want to open)
Add this to the godlike powers of Apocalypse, and it feels as though the writers want him to view non-mutants as insects. His pyramid of dominance (not the actual literal pyramid he was in) of strength puts him at the top with mutants below and ultimately Homo Sapiens at the bottom, but so far beneath his notice that they don't count.