Ward had no problem with being alone. It was how he grew up, how they trained him to be later. Up until the point he met her he was absolutely fine with being all by himself. He relished on the feeling, he liked the silence around him. Small moments of peace he could not get anywhere else.
Then he met Skye and his world got turned upside down. She kicked down every single wall he build, and forced him to see the colors he pointedly ignored. What surprised him more was the fact that he actually enjoyed her company, and the way she smiled, and the way she felt pressed up beside him when they pretended they were watching a movie. Well, she was. Ward just spent his time looking at her. Speculating how someone that had gone through so much could still hope.
But of course that didn't last long because like any other time he screwed up. He screwed up and followed John and Skye did not want to have anything to do with him. So the loneliness came back and he was alone once more. Only this time he did not enjoy it, he did not enjoy it at all. His cell seemed too quiet and the darkness wrapped around him too tight and Ward couldn't take it anymore.
He couldn't and he only had himself to blame.