It’s ambiguous and can be interpreted both ways, but if the author had wanted to be clear that it was qualifying the subject they’d have written

Tous les humains vous haïssent.

So if I needed to take a guess I’d venture that the intent was to qualify the object, purely based on inference, not grammar.

If, on the other hand, you wanted to clarify without the shadow of a doubt that it is "all of you" who are hated, you would need to work around it a bit, because Les humains vous haïssent tous is exactly how you’d say it if a slight doubt was acceptable.

You could say something like:

Les humains vous haïssent tous autant que vous êtes.

Les humains vous haïssent — vous tous.

Vous êtes tous haïs par les humains.

The first two are slightly more emphatic and the last one uses a passive voice.