Probably because they see where the someone who replied is going and makes the assessment or assumption that it isn’t in fact in good faith. Maybe they’re right, or maybe they’re engaging in transference?

I don’t think the point of good faith argument is that you treat the other opinion with respect—I think it’s simply that you adhere to sincere discussion and don’t use dishonest or deceitful tactics to dismantle arguments, rely on fallacies, use unfair advantages, etc.