It took at least a year for John to understand the touch of vulnerability and care that Sherlock had displayed around Sebastian Wilkes on the second case they had undertaken together. It's not that he didn't pick up on it, it's just that it took a while for him to understand how meaningful the little flickers of emotion from his friend were. At the time he hadn't known him well enough to gather that the small signs or the discomfort at his old fellow student's words were not usually shown on his face.
The doctor realised far too late that Sherlock was concerned that he would make fun of him or just run away when the banker explained what everyone used to think of him. John wanted to tell him that he was an idiot if he thought that the words of that man would sway him. He assumed he'd been clear with his "I thought bankers were all supposed to be heartless bastards" comment in relation to his feelings on the university acquaintance.
There were the hints at bullying and emotional exclusion of the past "we all hated him", but all of that just seemed to slide off Sherlock. It's easy to claim that that sort of thing doesn't bother you when you're a self proclaimed sociopath, but John eventually understood that those opinions and actions of others had shaped the man they saw before him even if he felt a majority of the comments had never got to him and hadn't mattered.
Sherlock isn't weak but he was shaped by the harsh comments and criticism over time relating to how his brain works and how he chooses to communicate what his mind offers. John has been able to help him gain strength and perspective and together they are stronger as people.