I had our quarterly inventory tonight at work so I don't know if this going to come off as coherent as I normally would be but here goes. And its almost 4 am.
I've reffed soccer for most of my life (since I was 12) and I can tell you this. I am currently grade 8 referee which is good for my local leagues (rec, high school, and regional tourneys) and only recently have I thought about upgrading so that I can do some more important tourneys and have my name out for games. The guys selected to do World Cup tend to be AT LEAST grade 3 or 4 (for lines) and 2 or 1 (for centers) I think. Meaning they have gone far beyond what I have even thought about trying as a ref. These guys are the premier referees in terms of exposure (top league refs, most well known, etc), physical, most respected, and knowledge/application of the rules. These rules are just to be considered for World Cup play, it doesn't guarantee a thing.
We as referees have hundreds of moments that we have to decide in a split second whether to apply "advantage", determine its bs, or make a call. A perfect example of this on the World Cup is corner kicks, its like holding in football... You can really call anything and be right. Soccer unlike the others, wants play to continue as much as possible. We can always come back to a foul if advantage does not materialize. It's the world's Super Bowl, you cannot be blatent with the corruption.
I saw the "foul" called PK in the Brasil/Croatia game and I must admit Croatia has every right to be pissed off about it. But I can understand why he called it. Ball in the box, early in the World Cup jitters, I've probably called worst things for PKs over my time (I probably tell the guy to get up). It was clearly a flop, but there isn't a review for him, there isn't 15 different camera angles for them to go back and say that's bs free kick Croatia. I'm certain he's kicking himself as he reviewed the game like most referees do (in all sports) for buying such a crappy flop and it may have cost him future assignments. The World Cup refs are guarenteed 1 match and based on the scores from that match and qualifying are then selected to do games in the Knock Out Stage.
Croatia has to look at itself too though, their goal keeping from what I've seen of the game is maybe a below average goalie. That first goal by Neymar was MAYBE a C grade shot, from that far out, it had little business going into the goal. PKs are like a free throw in the NBA, it's a shock when it doesn't go in. The third goal was even f'ing worse. Brasil also controlled the ball for most of the match (according to Yahoo 61-39), if you have that kind of discrepancy then there is a very clear difference between the two teams.
I'm not saying these guys couldn't be corrupted by politics, home cooking, etc we're just as human as any referee in any other sport. Our calls on that level is magnified by fact that so much of the world tunes in for this event SPECIFICALLY.