Looking at the rust belt states that Trump managed to peel off, I think she had two things working against her:

1. Her policies were less vivid and memorable. Her tax policy versus Trump's belligerence at trade partners Mexico and China where the factory work moved.

2. Her credibility regarding her ability to actually bring about change. I think Bill Clinton tried to address this in his speeches, but she is part of the establishment and therefore expected to continue the status quo.

This is apart from her health, which I think affected her ability to fight the media war, and being a woman, which makes her an icon for social issues whether or not she wants to be -- those maybe a factor but they are outside her control.