Two reasons. First, the crybaby "Bernie or nobody" crowd is currently tilting the polls, but most of them will come around once they get the last of the sand out of their dark crevices. Second, and much more importantly, because no one outside of the far left even knew who the fuck Bernie was before this election cycle, so he's never been under any real scrutiny. Clinton has been in the republican cross hairs for much much longer, so people have been conditioned by their rhetoric to have a knee-jerk negative response to her. If Bernie had won the primary, the republicans would have all started attacking him instead of Hillary, all the moderate voters who lean slightly right would realize how much about him they disagree with or even hate, and his poll numbers would drop like a stone. Americans hate socialists even more than they hate atheists (
http://www.gallup.com/poll/183713/socialist-presidential-candidates-least-appealing.aspx) and the republicans would have very little difficulty casting him as both.
Here, this explains it perfectly.
http://www.nytimes.com/2016/05/24/upshot/bernie-sanders-does-better-vs-trump-wouldnt-be-prudent-to-assume-that.html?_r=0