The age difference probably played a role in this. Dean was a figure of authority for Sam, and Sam was his charge. They had different experiences in being known. There was a four year age gap. Older siblings are incomprehensible. They have had a experiences that younger siblings can't yet imagine.
Sam in Fresh Blood tells Dean, “I've been following you around my entire life! I mean, I've been looking up to you since I was four, Dean. Studying you, trying to be just like my big brother. So yeah, I know you. Better than anyone else in the entire world. And this is exactly how you act when you're terrified.” This says a lot about Sam’s super-intellectual approach to life, but it also says something about the experience of the younger sibling at the outside looking in at the older sibling. Understanding an older siblings is harder than understanding a younger one.
Dean basically has four years of memories that Sam does not possess. He has memories of Sam the little baby, carrying baby Sam out of a burning house. He has memories of five-year-old Sam asking too many questions. He knows about Sam liking it when Dean did the airplane thing with the spoon. Sam had to work to know Dean. It doesn’t seem like the idea of working to know Sam crossed young Dean’s mind. Why would it?
Dean was, in many ways, very secretive with Sam. Mostly, it was John’s fault. We don’t talk about things in my family. We just make hell deals for each other. Dean kept secrets from Sam because that was what he was raised to do.
I think Dean felt a lot of shame about the secrets that he kept from Sam. Not the fact that he was lying to Sam. I don’t think young Dean realized that was a bad thing. Rather, the secrets themselves were shameful. The supernatural was shameful. The truth about his parents’ troubled marriage was shameful. What went down with the shtriga was definitely shameful.
There was a silence in the household. The things that Sam did not know. The things that had to be kept from Sam. The things Sam knew he did not know, the things that he grasped for in the darkness, knowing yet not wanting to know…
But Sam, little Sam, hid nothing. John and Dean both knew Sam. Even as Sam got older, and became more and more vocal about his wants and emotional needs…there was nothing to hide, as Sam was upfront about his needs in a way Dean never would have been. The one thing Sam might have to hide was his feeling of dirtiness and impurity. I mean, he complained to Dean in After School Special about being “the freak”, about everything he hated about their lives, but certainly not the full extent of his…wrongness. The feelings of uncleanliness he expressed in The Great Escapists.
So every part of Sam was known, his father and brother were mysterious and secretive, but he was known, except for one thing, the thing that Sam's hallucination of Dean expresses in WtLB: “You were always a monster. And you only feel right when you're sucking down more poison and more evil.[...]And I tried so hard to pretend that we were brothers. That you weren't one of the filthy things that we hunt. But we're not even the same species. You're nothing to me.”
When Sam tells Dean that Dean never knew him and never will, he’s not just articulating Dean’s fear. He’s articulating his own. If I didn’t know you, I would want to hunt you. But you don’t know me.
But Dean did pay attention to Sam growing up. Moreso than John, to be sure. Dean knows the surface stuff: What music puts Sam to sleep. What Sam’s hobbies were when he was eight, ten.
He knows the type of woman Sam goes for. “Monsters.” “Freak.” “Violent.”
He doesn't know that Sam believes in God.
Or at least, not the full extent of it.
“I do pray every day,” Sam says, and he has for "a long time", which is about the same length of time that Lenore and co. have refrained from killing people.
When? After Jessica died? College? As a teenager? How long? I would have asked. Dean, as far as we know, does not. As late as the pumpkin episode, Dean says to Sam, “I know you’re into the whole God thing, you know, Jesus on a tortilla and stuff like that.” He clearly has no idea what religion means to Sam, aside from the praying every day. He’s trying to convince Sam to hold onto that belief, that faith. Much as he wished Sam would never learn the truth about the supernatural, he wants Sam to believe in God - but he has no idea what it is that Sam believes, and displays no interest in learning.
We know little. We know Sam wanted to believe he could be saved. His family couldn’t do it, not in the long run. Jessica, who didn’t even know the world around her, certainly couldn’t do it. So he believed in God, and found redemption in his faith.
And maybe it was a secret. Maybe even to Jessica. Explaining that you need redemption requires an explanation of why.
And maybe it was good, to have a secret. Not a bad, dirty secret, but just a secret. A part of yourself that no one knows. A part that no one needs to know. Not bad, just…secret. “I do pray every day.”
Was Sam praying, that summer Dean was in Hell? Fucking Ruby, and then praying to God afterward?
You don’t know me. You never did. And you never will.