I don't think it was simply a question of Brazil being mentally unprepared.
The bigger problems were lack of defensive cohesion, and lack of offensive capacity to breach Netherlands' defense.
The defense problem was the worse of the two issues. Whether that was caused by lacking player material or poor management and tournament preparation, I can't say. Maybe Brazil's football culture has not focused on grooming defensive talents, maybe Scholari didn't manage to role the team correctly. Brazil showed signs of the defense problem all the way through the tournament but it all finally came apart against Germany. In the Bronze game, they fared a bit better but the underlying problem was still there and was a factor in all three goals. Silva was playing, so maybe that had a bit of an improvement in their defense line-up.
As for lack of offensive capacity against Netherlands' defense, it was a combination of Netherlands having really solid defense, blocking the midfield and pass lines, and Brazil's players not being quite able to play together. Neymar being out was probably not a big factor. There were a lot of individual attempts, which failed. And when they tried to play as a team, they misread each other and passed too long, or otherwise misplaced their passes.
After the second goal, Netherlands seemed content to sit back and defend, they left the ball in Brazil's possession but they couldn't really do anything with it. Almost every attack ended in misplaced pass, losing a challenge and the ball to Netherlands, or individual shots on goal which Cillessen either caught or they went past the goal. They had a few corners and free kicks that gave them a chance, but in the end they didn't even score a single goal.
Looking at the replays it was pretty clear that the first penalty kick should have been a free kick and red card instead of a penalty and yellow card. I doubt it would have actually changed the game's result, but Robben was pulled down outside the penalty zone even if he fell into it. I was surprised to see a penalty from that situation.
