I think it's a little of both. Most people would have been very surprised if Trump had lost but been at like 250 electoral votes, getting that close. I think he deserves some credit for being in it, but you're right. Her base failed to turn out in those Midwestern states. I don't think she inspired the confidence in all minority groups as people thought she would. The Hispanic/Latino community seemed to be the most motivated for obvious reasons.
EDIT: I also think a lot of the people who identify as independents are really Republicans who aren't comfortable with the party's stance on social issues.