Munich was a flop, but it wasn't a spectacular flop. It only cost $70 million to make, can't really spectacularly flop with that small a budget. And of course it was one of Spielberg's "no really I'm a serious director" movies, those tend to not make much money, but they rev Spielberg up for another one of his license to print money movies. Check Spielberg's page http://www.boxofficemojo.com/people/chart/?view=Director&id=stevenspielberg.htm
Lots of loss leader "serious" movies followed by a tidy little blockbuster, and frequently the company running the cycle is Universal.
And of course the other big difference is that when Spielberg makes $200 million on a movie he doesn't spend $200 million to make it. Remember it's all relative to the budget, Saving Private Ryan got 2 million less domestically than Kong, but cost 1/3 as much to make. The difference between a $216 million dollar grossing hit, and a $218 million dollar grossing pink slip is $140 million in budget.
But it's going to take years to make that money back, even after a theatrical AND DVD run. In its lifetime, it's made 47 million, and it cost 70 million. That's a big loss, because it has no interest to KEEP making money. It's no longer in theaters, and the DVD run has been going on for some time, so it is going to gradually trickle in the dollars over years of time. Even among serious "Oscar-contender" movies, that's pretty bad. It's much worse than most other dramas of its ilk.
Kong has more than made back the money it cost to make, and is continuing to reap in a fortune for Universal. You seem to want the movie makers to apologize for their gigantic budget, but hey...it's a humongous monster epic made by a guy who specializes in special effects-filled events. Why NOT have a 200 million budget, and make it as amazing as possible? That's the type of movie it is.
(I could be wrong, but I think "Superman Returns" would be a better example of what you're trying to illustrate. It had an even BIGGER budget than Kong, and didn't even break 200 million in the box office).