Love the story so far. I really do like your characterizations of the entire family. John is a hard character to write well. So often people portray him as being a real bastard. I think his heart is in the right place most of the time. He keeps a watch out for Sam when he's at Stamford even if Sam didn't know and bragged about Sam's achievements to other people even if it wasn't to Sam. It's obvious that his sons are not afraid of him, and don't have a problem hugging him in Chicago so physical affection (on a totally appropriate level) is not unknown to them.
But a lot of the times John has really screwed up with his kids. I don't think he communicates that well with them (which is not a surprise when it seems that he has had arguments with most of the people who were at least once his allies), and he puts far too much burden on Dean's shoulder for taking care of his brother when that should be John's job. The way he leaves them for days at a time in just a motel room would be considered child abuse in most places that I know. His obsession can make him overlook the damage he's doing to his sons.
So (after an unnecessary character analysis) writing him as somewhat sympathetic character who usually comes across as a hard-ass but with good intentions is hard to do. Particularly, without long or lots of paragraphs that explain his thoughts process which just seems out of character for him and can really bog down a story. Don't feel discouraged if you have a hard time with him. You do it well.
With regards to be people not commenting on a general story. Of course, some people focus on one type of genre over another. But in my case, I didn't see this on some of the boards that I have seen your other stories, i.e. Cry Wolf, that I check on a normal basis. I only ran into it yesterday because I periodically go to the individual's site of some of my favorite writer (which you are one).
Anyways, I hope that you post another chapter soon.