Well, I'm not an umpire - but I've been around enough to offer some advice...
You are going to come across umpires that seem to be over the top, aggressive, ticked off, etc. This may or may not have anything to do with your team. The may have had a rough game previous to yours, may have had a fight with their wife - whatever. It could be something your team did, who knows?
The important thing is to realize that doing anything to further fuel the fire isn't going to help at all. Best thing to do is to keep quiet, and just play the game. Afterwards you communicate the situation with whoever is in charge.
With that said though, while the umpire is certainly entitled to his own judgment - he is not entitled to his own rules. If he feels a pitcher intentionally threw at a batter, he is certainly entitled (if not obligated) to eject the pitcher. However, when the ball hits the batter it is dead. Runners return if not forced.
In that case you needed to ask him to clarify his ruling. Then tell him that you think he is interpreting the rule incorrectly. Depending on the tournament policies, if he did not change his ruling, you should have followed whatever the protest procedure was.
In all honesty, after a decade or so of coaching various different age levels, I've never had to actually protest a game. Usually once you inform the umpire of your plan to protest, he will confer with his partner and either realize his error, or they will both explain your error. (I've had it happen both ways)