It was because of Nate Silver's track record that I initially had high confidence in his estimate. Then as I read his justification my confidence in his estimate decreased. I think he's just being lazy in his justification, here, when he says things like:

So, how do I wind up with that 2 percent estimate of Trump’s nomination chances? It’s what you get if you assume he has a 50 percent chance of surviving each subsequent stage of the gantlet.

To be fair to Silver, when he wrote the article he might not have considered Trump's campaign plausible enough to give serious thought. I suspect that if Trump continues to perform well in the polls Silver will give a more thoughtful and realistic analysis later on.