There were a few things that made the US team vulnerable.
While that first line buzzed against most competition, they weren't necessarily elite. Compared to Canada's team who had Kent Johnson, Mactavish and Bedard, the US team was a few levels below that. I'm not sure there was a single US forward that I think is a sure fire future NHL first line player. Even Knies strikes me as a middle six forward at best and he was like there most skilled forward.
But the biggest issue facing the US team was their size. Compared to the other teams in the tournament they were small. The Czechs had a huge advantage in that dept and took away time and space when they got the lead. You could see the US team getting frustrated and also banged up throughout the game. The US team hadn't really played from behind and against a much more stout team it was their achilles heel.
The Berard penalty, as stupid and bad as it was, was a real indication with just how frustrated the US team was. They just couldn't do much once they went down. Of course, Hughes getting banged up really hurt them as it basically took away their most skilled player.
Point being it was not the most well constructed team. Though, there's only so many options year in and year out when picking an age-specific squad.