I actually personally think if it weren't for Kaine, she might have actually lost Virginia, in the early returns it was leaning for Trump, but she came back to win it later on.
That happens every election cycle with Northern Virginia coming in last.
Yes compounded by the fact that rural VA swung hard against Clinton, just like rural areas all over the country did. Trump got blown out in NOVA as expected, and even though VA wasn't called until late in the evening, Clinton actually ended up winning it by about six points. Really it's just a more extreme version of what's happened in every election in Virginia since 2006.