RealClearPolitics was accurate: they predicted Clinton would win the popular vote by 2%, which she did and which your link shows. I see no reason to assume they were wrong about Sanders.
The Dems hit Sanders hard for being a socialist during the first three month. It didn’t work, so they changed course. They never treated him with kid gloves. As Wikileaks revealed, they did everything they possibly could to destroy him. They had no reason to treat him with kid gloves—the party establishment wanted Clinton.
Clinton rarely polled better than Trump by more than a couple of points—she was almost always in danger of being defeated by the Electoral College. I think the only time she polled stronger was after Sanders conceded. Sanders’ margin always made him the safer choice.
Really, you only have to spend a little more time at RCP to see this.