John couldn't lead them, which was different for him. He wasn't used to waiting and relying on Sam's plan. Whenever he came about he was always taking control. But with Mary gone, he was compromised and Sam had picked up on it. Whether or not he was aware he did or not and taken the lead. He was worried for his wife, and at the same time for his kids. His family was his weak spot. He knew it, they knew it. They were taking advantage and John was letting them see it getting to him. He needed to stop, he knew that. So he focused on being there for Dean. John knew Dean was suffering even if he didn't show it. Dean had been close to his mother before she was taken away from yellow eyes in the first place. He had memories Sammy was just too young to remember. So that's where he and Dean connected.
Secretly he needed that connection too. Someone to keep him from flying off the handle again. Dean had always done that for him. Even when he was a kid and John should have been telling him that things were okay. Not the other way around. His eyes traveled toward his first born, but he kept walking. "She's tough, Dean. We're not going to lose her again." He tried for reassurance and hoped his son picked up on what he was going for without further explanation.
John didn't like the newer model of Dean. The one who would loudly defy him and go against orders if he felt he needed to, but there was no use mourning the loss of that son. He would have to adjust and he knew it. Dean wasn't just a soldier anymore, he was his own person.
Most parents would want that for their kid, but John wasn't the typical father. He wanted things to go smoothly, but with Dean testing him every step of the way lately it wasn't easy.