Because the polls were wrong. Or, at least, incomplete. It doesn't matter how good your algorithms are if the data isn't there. And 2016 proved that 538, and really most media outlets, don't have a grip on America.
In other words, the existence of a black swan event in that particular system didn't really matter.
Silver is a glorified modern fortune teller, who seems to have deluded himself into thinking that simply having data means you can prescribe meaningful probabilities to the future. Assigning probabilities to a coin flip is easy. Figuring out the most likely winner of a game of baseball is a little harder; there's a whole movie about a guy who was basically doing that in 2002. Politics is a completely different field. You can't possibly assemble all of the data necessary to be remotely confident in the probability of outcomes. And let's not forget unpredictable black swan events.
But the readers love it. And, especially during the elections, the media would bring him out like a golden boy computer whiz, because he was saying the same things they were, but he's really smart and has the data and magic algorithms to back him up. And he was right that one time 8 years ago. He's about as pointless as Sean Hannity, with the one exception that, at least recently, Hannity was actually more correct about the future than Nate. It doesn't matter if you are right or wrong, if the reasons are wrong.