Several people criticize the way Dean reproached Sam for leaving for Stanford, saying it was completely unfair to Sam. I agree with that; however, Dean's perspective is often overlooked.
When I consider Dean's behavior and perspective, I realize it’s similar to a situation I went through when a close friend of mine left. While I surely didn't experience it exactly the same way as Dean, the feelings were quite similar, which helps me understand him better and see the reason behind his actions since I reacted in much the same way he did.
I'm not saying what he did was right or that Sam deserved it or whatever, because that's not the case at all. I simply want to analyze Dean's behavior by comparing it to my personal experience.
First, there's the element of surprise. Sam probably didn't mention his intention to go to Stanford before the night that ended with him leaving for college. When I found out my friend was leaving, she had only one day left to pack her things. The shock of such upsetting news being so sudden can cause a long-term resentment. It doesn't give you enough time to process what’s happening. You don't even have time to discuss or understand it, because next thing you know, the person is already gone, and you can't do anything about it.
This leads to a feeling of helplessness. Someone you are very close to leaving you impacts your life. Even if the other person makes the decision to change their life for the better, their actions will also bring changes to your own life (mostly in a negative way). You don't want the person to leave because you know it's going to be bad for you, but it's not your decision; the other person chooses to leave anyway, and you have no say in the matter. You are forced to endure the consequences of their choices, to feel bad because they didn't consider what their actions would do to you. This sense of injustice and helplessness causes anger. Dean must have been angry at Sam for doing what seemed best for himself because he didn't consider how it would affect Dean. It seems like they don’t care about you, because leaving you behind, hurt and scared doesn’t matter as long as they’ll get to live their sweet little apple pie life.
After the person leaves, you feel betrayed and alone. Those who promised to be there for you are not, sometimes it seems they have no memory it ever happened and other time they only make you feel worse (I can see John acting as if Sam never existed or to talk shit about him when Dean didn’t wanted to think about Sam).
Even if you know it's not fair to blame them because they did what was right for themselves, you can't help but be angry at them because what is good for them hurts you. By listening to their own needs, they deprived you of your happiness. It's as if they had to choose between you and themselves and chose themselves. Even if you know it was the right thing to do, you can't help but find them selfish, because you can’t control how it makes you feel.
Even if your mind understands and accepts their actions, your heart doesn’t, and unfortunately, it's often emotions that drive actions. I know that sometimes I was unfair to her, wanting her to feel guilty for how she hurt me and to regret her choice. That was probably also why Dean reproached Sam so much for leaving; he wanted Sam to feel guilty for hurting him. Dean is not stupid; he knew Sam's choice was the right one and even told him he was proud of him for making it. However, he can't forget all the pain it caused him. Even after years and forgiveness, this kind of pain leaves deep scars.
I think Dean understood Sam's choice; he agreed with wanting to have a normal life. However, the pain caused by Sam leaving him behind, the fear, and the helplessness predominantly influenced his behavior.