I don't think there is anything wrong with "getting into" a game. Nothing wrong with cheering for your son or yelling "come on blue" on what you perceive to be a bad call. In my opinion, that is part of what makes a baseball game fun. I do it for other pitchers as well as my son.
This thread in particular is talking about THAT dad that boosts up his son in front of everyone and that's all he talks about - how good his son is - ad nauseum. I know there is another thread out there about out of control parents that insert themselves into games. There is a big difference between overboard and being "into" the game and rooting for your team (and your son). Baseball is a competition and part of the thrill of watching it is to want your team to win. Part of the thrill is cheering your team (and your son who is part of the team) and yelling at the umps occasionally.
I don't think people need to go from one extreme (overboard yelling and screaming and inserting the fans into the game) to the other (sitting quietly and stoically not saying anything). There is a balance and I think that middle ground makes the game that much more fun.
This is just my opinion. Be a fan - root for your team - including your son.