In the year before Sam was born, John and Mary's marriage had started to get rocky. The start of their lives together had been marked by incredible tragedy, but they had managed to pull through and grow stronger together through the years that followed, including the nearly five years of trying before they had Dean. That year however, it was beginning to look like they were heading towards divorce as habits that the other had found endearing in the beginning just became annoying. The main reason for it however probably had to do with the fact that every time John had tried to get Dean to do something, the boy who had just started speaking in coherent sentences would say "I don't have to listen to you, you're not my dad!". This rather stung John because he'd suffered an injury during the war in Vietnam and had been told that it would be unlikely that he would have any children, hence him being somewhat wary of the miracle of Dean's existence.
If Dean hadn't looked so much like he had as a baby and as a toddler, albeit with much lighter hair, and if Dean had had a different blood type when he'd had him tested, he would have divorced Mary then and there. However, Dean resembled him to a degree, and they had the same blood type, so he couldn't rule out Dean not being his child as the doctor hadn't been a hundred percent certain that he couldn't have children. He wouldn't leave Dean if there was a chance that the boy was actually his son.
Since the private investigator that he had hired hadn't found any evidence of infidelity on Mary's part whatsoever, John was less wary of the new miracle that would be arriving when Mary had informed him that she was pregnant once more after nearly three years of trying for another child. With this news, he relaxed, believing that the doctor who had seen to him after he'd been injured had been wrong.
After Sam was born, Dean quit going through his "You're not my dad" phase, as the boy who had been far more attached to Mary than to him had found someone new to latch onto. That new person being Sam whom Dean loved absolutely and unconditionally. Dean had pretty much fallen in love with Sam in the instant he'd first laid eyes on his baby brother at the hospital shortly after he was born. Every day after that was all about Sam.
As the years since Mary's death passed, Dean became an obedient and loving son. The one Dean was most loyal to however was his little brother Sammy.
When Sammy was three, he too went through a "You're not my dad" phase. Sam's was different however. Rather than refuse to listen to him, Sam had commented on how glad he was that he wasn't his father since his father hated him and locked him up. This had gotten him some odd looks when Sam had said that to him in front of witnesses.
At this point, John wondered if it was a phase that all toddlers went through, much like that sticking everything they could get their hands on in their mouths phase they went through when they were babies.
At the end of the eighties however, John decided to double check with a new test that involved something called DNA. When the results showed that both Sam and Dean were his children, he put their "You're not my father" phases out of his mind as something childish. He was their father after all, the exceedingly expensive tests had proven it.
In January 1990, an angel who couldn't take it anymore quietly fell, landing in a small town called Windom, Minnesota, and a woman who had been told a year earlier that she couldn't have children was surprised to discover that she was expecting a bundle of joy as a result of a one night stand she'd had with a guy she'd met at work.
Years passed, years in which Dean became the obedient son and Sam the rebellious one. Years in which Sam and Dean grew very close, drifted apart, and grew close once more after Sam suffered a loss and went back on the road with his brother. Years in which John died, Sam and Dean became inseparable, and Dean willingly died for his brother.
If Dean's soul looked a bit different to the other souls in Hell, Castiel chalked that up to the fact that it belonged to a man who didn't belong there. If Dean seemed to understand what he was saying, even though his words were practically killing his newly reconstructed body, Castiel chalked it up to the fact that Dean was to be Michael's vessel and was therefore special somehow.
There was no reason to suspect that Dean was anything other than Dean as there was no reason to suspect that Sam was anything other than Sam.