CNN, WP, and NYT basically do just present the facts in their reporting. To the extent that it's a big deal when they put out a falsehood and people have gotten fired. Opinion sections are obviously different.
The Clinton campaign specifically asked the news media (including CNN, WP, NYT) to increase coverage of Trump (as well as Carson and Cruz). This is so that they'd either have someone easier to beat in the case of these 'pied piper' candidates, or pull a stronger opponent farther right come the general.
Nate Silver didn't know about this in March of 2016 when he wrote that article.
Don't like Trump? Thank Hillary Clinton, the DNC, and the media for playing along.
The news is almost all factual but is meant to swing a person's opinion in just about every way without actually citing false facts (unless the subject is WMDs in Iraq). It is probably the best TV news source we have in the US but it still sets a fairly low bar in terms of objectivity.
Oftentimes, just leaving out certain facts while including others can have just as much of an influence as citing false facts outright, especially when done repeatedly.