DEAN: Kind of makes you wish he knew the truth, huh? I mean, all those years thinking his old man ditched when the poor son of a bitch really came here and saved our bacon. Freaking time-travel, man.
SAM: You think it would have made a difference?
DEAN: What?
SAM: Dad. If he'd had his own father around.
DEAN: What, in how he raised us? Sammy, he did the best he could.
SAM: I know that. I – I do. They all did.
Dean has absolutely been thinking the same thing Sam's saying out loud this entire episode, is the thing. Sam's played nice with Henry, but Dean wouldn't even shake his hand, because Henry was the guy who abandoned their dad.
DEAN: I'm just saying before we break out the warm and toasties, let's not forget that, uh, H.G. Wells over there left Dad high and dry when he was a kid.
SAM: But maybe he didn't run out on Dad – I mean, not on purpose. Maybe he time-traveled here and, I don't know, got stuck.
DEAN: Yeah, well, either way, Dad hated the son of a bitch.
SAM: And Dad made up for that how? By being father of the year?
Initially, I thought Sam's response was odd, because the fact that John neglected them doesn't excuse Henry abandoning John. But Sam's clocking here that Dean sees Henry's abandonment of John as a catalyst for John abandoning them, and Sam is actually saying John's behavior was all on John, and if anything, he should have known better than the average person how damaging it is to abandon your children and been more present. Dean then reacts to that by insisting, "Dad had his issues, okay, but he was always there for us." But we know that isn't true based on everything Dean himself has said in the past and everything we have seen as viewers. Dean criticizing his father is well-documented. (I also have specific tags for Sam's relationship with john and Dean's relationship with John where I expound on all of this at length/Sam and Dean's feelings about John and changes in those feelings throughout the seasons). Saying John "did the best he could"/"did his best" is actually a repeated Sam line (1.08, 2.03, 5.13, 14.13). This is the first (and if iirc only) time in the series that Dean is the one to use this phrasing (don't believe me? search here!)
All of that to say... there is no reality in which Dean's grudge against Henry throughout the episode was not at least partly driven by the belief that generational trauma has screwed their family to hell and Henry abandoning John was part of what lead John to leave his children alone in motels for days at a time when they were very very young, and ghost them for the sake of The Mission. This is also why Dean yells at Henry specifically for putting his mission over his child (the same way John put revenge over them until 2.01).
The thing is that Sam and Dean are both getting older, and they're emotionally further from their issues with their dad, and they're reevaluating what they experienced as kids as a complex web. Dean starts the episode with his anger focused on Henry as a first domino, while Sam (in an interesting twist if you know what his comments about John have largely been like since season 2) denies him the excuse. But they both soften. Dean starts out feeling more conciliatory toward John and softens on Henry, while Sam starts out feeling more conciliatory toward Henry and softens on John. At the end of the episode, they are both left contemplating Henry and John and the Winchesters and Campbells in general for generations as victims of a complex web of heavenly machinations.
