This is cut throat sport folks, this is not some gentlemen's society fun golf tournament. It's about winning - that's what they get paid for.
If Sagan didn't want to get played like he was then he needed to race smarter. It's not enough to be the strongest. Cycling is the sport were being strongest doesn't guarantee the win, and that's surely what we all love about it.
It's true, that being strongest, isn't a guarantee to win. But you surely don't win, if you sit down and roundtable who needs to do the next pull. There was no time to race smarter.
Kwiato went to the front once or twice, but besides that he let Sagan do all the work. Kwiato either didn't have the legs to do more work, or he was willing to sacrifice their gap to the peloton just to increase his chances to outsprint Sagan on the line. Either of the two doesn't make Kwiato a champion. It makes him a winner, but not a champion.
Sagan sacrificed it all. He even gambled his own chance to win the race just to make sure that he at least made the podium. That's the heart of a true champion, and that's the kind of thing that spectators love about the sport.
Racing is about winning - yes. But it's more than that. There are wins, and then there are great wins. This wasn't a great win IMHO. Last years MSR wasn't either. Froomes downhill attack and win at the 2016 TdF stage 9 was a great win. Sagans 2016 Tour of Flanders was a great win.