I really don't think the referee was bad. He made some mistakes like that corner he did npt give, but that kind of mistakes happen in every match. Maybe not such clear ones, but in every match the ref and assistants make mistakes regarding corners or throw-ins.
I think he did right not to send off Van Bommel for his tackle on Iniesta, but De Jong was of course lucky to play on. He was handed an awful lot of nasty situations to handle. Many a ref would have lost control totally, long before the game went into extra time.
Warhurst said:
The ref being close to the situaton says no foul. The ball is away and the Spanish player takes revenge. Th reff sees it and gives the Dutch a free kick. I say at least a yellow card and perhaps (if he was kicking or hitting) a red card.
I'm actually not sure he sees the situation really well. As you say, the ball is away - and if you watch the replay closely you'll see that the referee follows the ball with his eyes. It is the linesman who signals a free kick. I agree it should have been a yellow (from the replays it was quite clear that there was no kick or punch, thus no red card).
The second half as well as extra time were very exciting. Both teams seemed to lose defensive structure as the match went on, starting with Robben's huge chance after 60 minutes. How did he miss that? Casillas was already on his way down when Robben let off the shot.
All in all, what made the difference was that Spain took one of their chances. Netherlands did not. Spain were the (slightly) better team, and the third country in history to be holders of both the European Championship and the World Cup (after West Germany and France).