The infamous John Winchester makes a corporeal visit in this episode, at least for the viewer. Dean and Sam have to rely on a telephone call, but at least it's "live" and not voice mail.
John was very "fatherly" at the beginning of the phone call with Sammy, assuring his youngest that he was all right, then asking after Sam and Dean. Then John lets the viewer (and his sons) know that he has been keeping up with Sam and Dean by expressing his sorrow at Jess's death. What John doesn't mention, though, is Dean's "death" in St. Louis from "Skin" or Dean's phone call asking for help in "Home", which by viewer's accounts, happened two weeks ago.
John tries to deflect Sam's queries into what he's hunting, finally losing his temper at what he considers pestering questions. John called for a reason, and it was to give them a job to do. John started off being the concerned parent, and I believe that was an honest moment for John, but he and Sam degenerated into their bickering within two minutes of talking to each other.
While John is still part concerned parent, stopping evil from killing innocents is his priority. For all of Sam's leaving the family to go to school, Sam was certainly eager to join John in the hunt for the demon. None of the worry that dad wouldn't want to talk to him ("Bugs"), or staying gone ("Woman in White") from Sam; just determination to be with John.
And John was just as determined to keep Sam and Dean away from him, telling Sam it wasn't safe, that "they" were everywhere, and not even the phone call was safe. He's still trying to protect his boys, but he wanted to let them know he was all right. And, to send them to Indiana to stop another couple from disappearing.
Dean takes the phone from Sam when it's apparent that the conversation with John isn't going to progress, and within seconds, Dean's back straightens and a "yes, sir" is out of his mouth. Interesting (and extremely annoying) that we don't hear what John says to Dean. Did John give Dean any assurance that he was okay? Or did he immediately jump into the explanation of Indiana?
From Dean and Sam's conversation in the car on the way to Indiana, I'm guessing John imparted a lot to Dean in the few minutes he was on the phone with his eldest. Or else John and Dean have a sort of "code" they can speak in, since they understand each other: take these names down, small town in Indiana, cross country trip, disappearances.
John's still "between" the boys as Sam stops the car in the middle of the road. Sam questions Dean's "blind faith" in John, while Dean calls Sam a "selfish bastard". Dean sees himself as the good son, doing what John tells him to do without question, in their mutual efforts to save lives. Sam sees Dean as weak, following orders like a dumb soldier, never asking "why" or having a mind of his own ("Asylum"). I do think a lot of Sam's outburst from "Asylum" continued in "Scarecrow" in regards to John and Dean. It's obvious the subject of John Winchester is a sore point between the boys, and as Sam leaves Dean on the side of the road, heading to Sacramento (and how big is that city again??) to find John, we see the first major fight between the boys.
At least they're both passionate about their feelings towards their father, even if those feelings are nearly polar-opposite. In some way, that's better than them not having any feelings towards John at all. That probably points back to the way they were raised, and how John treated them to invoke that much concern toward him, but that’s another post *g*