i love that the episode about secrets comes immediately after the episode about fear. because if dean's fear is of losing his family and being alone, then this scene carries incredible meaning for him.
because secrets keep people apart. they're a rift in a relationship, a gap that can't be crossed. that gap leaves an uncertainty in the relationship, a lack of trust, a space separating two people. if dean is afraid of being apart from his family, then secrets are a threat to his security.
and to that end, dean's shock at the notion that sam hasn't told dean everything implies that this isn't a normal occurrence for them, that it's typical for sam, at least, to be open and honest with dean. if that's the case, then sam's college excursion has changed his attitude toward his brother, put some distance between them that dean clearly doesn't like and, based on the scene and what is later revealed about his character, has a hard time coping with.
this is the first time dean really makes an attempt to exert control over sam. he puts his foot down and tries to take the reins, and importantly this happens immediately after the security of his relationship with sam is threatened (or at least, he perceives it to be that way). this becomes a recurring theme throughout the series, so these early signs of this behavior pattern become retroactively strengthened through hindsight.
it's an interesting follow-up to phantom traveler, because now that seeds of doubt and conflict have been planted in dean's mind, his sense of security is breaking down and his fears are growing. sam is trying to put himself in harm's way, which could kill him: dean could lose sam in a very physical way. sam is keeping secrets from him, which is keeping them emotionally distant: dean could lose sam in an interpersonal way. his fear of losing his brother is being dangled twofold in front of him, and the threat of losing his dad is looming over them in the background.
the ground is crumbling under dean, and so he reacts the only way he knows how: by trying to take control of the situation, to protect his family and keep them by his side.