"Nestor looked down at him" (here I mean that Nestor stood higher). "Nestor looked down on him" (here I mean that Nestor treated him as rubbish). Am I right?
It depends on the context. "I stood on the mountain and looked down on the valley", This doesn't mean that I thought any less of the valley. "He looked down on the workers" - this could mean that he felt superior to the workers, or, that he was physically above the workers.