Twenty-two years ago, John Winchester was a regular, normal father and a husband and he became something else entirely the night his wife died, pinned to the ceiling of their younger son's nursery. What that meant for his sons and himself isn't exactly clear in the pilot of Supernatural, but based on what the boys tell us, we can make a few conjectures.
The flashback that begins the episode tells us a lot about John as a father before his wife's death. Four-year-old Dean seems incredibly glad to see his dad when John comes into the nursery, presumably to put Dean to bed. They talk about football, and John holds his son close, and it's apparent that he dotes on the boy. There's no sign that he's a particularly stern daddy, one that his son might approach with a little less enthusiasm and a little more deference. His parting "Sweet dreams, Sammy," is caring and gentle. By all accounts, a loving and involved father.
After Mary's death, we aren't given much about John as father figure until Sam and Dean's discussion in the stairwell:
SAM: When I told Dad I was afraid of the thing in my closet, he gave me a .45.This says a lot not just about Dean as hardened hunter and Sam as uncomprehending son, but about John as disillusioned father. He can't tell his son not to be afraid of the dark. Given the manner of Mary's death, he never had a normal parent's blind faith that he could keep his children safe. He couldn't--not if he could lose his wife in such a horrible way, right in the center of domestic safety, a child's nursery.
DEAN: Well, what was he supposed to do?
SAM: I was nine years old! He was supposed to say "don't be afraid of the dark!"
DEAN: "Don't be afraid of the dark," are you kidding me!? Of course you should be afraid of the dark. You know what's out there!
Sam laments that they were raised like warriors, but I'm not sure John could have done anything else, given what little we know of him in this first episode. He was a marine, as evidenced by the photo of him in his BDUs and his USMC t-shirt (not to mention that Dean actually names him as an ex-marine later in the episode), and it's entirely plausible to assume that once he began digging into his wife's death, he'd have gone into "protect and serve" mode pretty quickly when it came to his sons.
Now, any discussion of Dean's perspective aside, I also think that John would have held Sam a bit closer, been more protective and less companionable with him. Treated him like a son. The shot of John cradling his six-month-old infant in his arms while his family home burns tells the tale. Dean was old enough to know what was going on--to remember the heat and fear of his mother's death. In a marine's mind, this might have looked like the ultimate loss of innocence, because Dean watched the aftermath with understanding eyes. But Sam was still a true innocent: too young to understand what was going on, and therefore to be protected more completely.
And perhaps that's why Dean stayed and Sam left. Perhaps that's why Sam rebelled and John retaliated. I've already discussed Dean's role in the family as the boys grew up, but what about Sam's? Well, sticking to the pilot, I'd say Sam's role was that of cherished son. Yes, he was raised as a warrior like his brother, but I think that the very fact that he had the separation from his father necessary to rebel is a sign that perhaps John held him a bit away from the action.
It's apparent that John rejected Sam's plans to attend college--even going so far as to tell his son that, if he left, he wasn't to come back. But I think, even in the pilot, we can read that as fear as much as anything else.
After all, Sam evinces surprise when Dean tells him he was dealing with his own, separate, hunt when John went missing. "Dad let you go hunting by yourself?" he asks incredulously. Because I think John was afraid to let his boys too far out of his sight, at least while Sam was at home. Why that might have changed is a subject for a different meta entirely *g*.
So John's obsessed not only with finding this demon, but, seemingly, with keeping his boys safe, and in the pilot, John's obsessions are already characterized as all-consuming. Who but a man truly obsessed with vengeance and the safety of his children would raise his sons to protect themselves by killing demons and ghosts, yet try to deny one of them his dreams of a normal life?
And here's the deal with John Winchester and the raising of his sons: I don't think, given the look on John's face as Mary burned, that he ever truly believed in normal again after that. Normal was what happened when people weren't on their guard. Normal was what he thought he and Mary and their two beautiful children had, and look how that turned out?
I think that John must have felt that Sam leaving to pursue a normal life was Sam leaving himself open to the horrors that normal people don't know about. "We're all in danger," John tells Dean on the voicemail that begins Dean and Sam's hunt for their missing father. And I think he's always thought that. Safety in numbers was quite likely his rule of thumb, so when Sam suggested leaving the pack, John lashed out, and drove his son farther away.
Which is a typically fatherly thing to do, by the way.
Because I think popular characterization of John as taskmaster and slightly callous drill sergeant misses the point that he, as a father, needed to keep his boys safe. Yes, he's obsessed (Sam and Dean both seem to agree on that point) and yes, he raised his boys in a way that most would call bad parenting, if not outright abusive, but it was all done out of the knowledge that was in his eyes as he and his sons watched their home destroyed twenty-two years ago.
His sons could never be safe, even if he was with them, but at least, keeping them close, he could do something.