The San Francisco 49ers are officially a train wreck. There are certainly some areas where things are not entirely bleek (Andrew Tiller, Aaron Lynch, Jaquiski Tartt, Arik Armstead, for example), but from a big picture perspective, things are not good. The 49ers almost beat the New York Giants, and then did beat the Baltimore Ravens, but those games were red herrings in this season. The team has talented players, but overall, they are a bad team.
A different way to put it is that this a bad organization right now. Just like there are good players on the roster, there are good people in the organization.