Despite his softness, weakness and oddness (specially with that nerdy-look), being bullied at school (specially by Homer Simpson) and beaten by Alfred Spencer... deep inside Waylon Smithers Jr. it's the most bravest and strongest child. He found the reasons for endure and defiance that awful life. The most strong reason is the vision of Mr. Burns' warm smile, the only person who give him happiness. So that's why Waylon have this hidden courage for face everything.
With more reason. I have the vision that even in his adulthood, Smithers treasure the memories when he was a child and lived with Monty. That vision of that warm smile and those mournful eyes (in those days, Smithers Sr.'s death was still fresh in Burns' memory) that show him the real side of his current boss; so not matter if now Mr. Burns is awful and even threatening with him, Smithers know this secret and real side; for it he keep loving him.