How I'd rank the theories:

1. The Clintons have been the targets of a well-funded and well-organized smear campaign since Bill's first term. It's not personal; they're just the biggest targets of convenience for the right wing political machine. The result is that large sections of the electorate have been trained to hate the name for a quarter of a century.
2. Hillary's record as a decision maker is genuinely bad. From supporting Bush's war in Iraq, to hiring (and not firing) incompetent people during her first primary run against Obama, to taking $600,000 per speech from Goldman Sachs while critics were accusing her of being in the pocket of Wall Street, to Benghazi, she's consistently made bad calls.
3. Identity politics: I don't think the Democratic leadership grasps how racist and sexist they seem to most Americans outside the left wing bubble. Just because the racism is directed against white people, and the sexism against men or straight people, doesn't make it less off-putting.
4. Bernie. His campaign stripped her of at least some support, and a lot of momentum. Also forced her to the left.
5. Trump isn't a very funny guy, but he's funnier than Hillary. As Judd Apatow oberved, the funnier candidate usually wins.