I mean, this has Heller as less popular than Trump and Trump lost Nevada to Clinton. Why would Heller then be able to beat a halfway competent candidate tailored to the state?
For the same reason so many people think Donnelly and McCaskill are favored: Incumbency.
I can't speak for those who think Donnelly is favored, but that's not the reason I think McCaskill is favored. In 2012, she significantly outperformed her polls. The RCP average had her up 6.3%, she won by 15.7%. She seems to be underrated.