TPM's John Judis has a decent set of hypotheses:
This year, Trump proved anything but hapless, and Clinton ran a campaign that sadly recalled Gore in 2000 and Dukakis in 1988. She was unable to distinguish her own approach from Obama’s – particularly on the explosive issues of Obamacare and immigration. She ran an almost entirely negative campaign focused on her opponents’ bigotry, sexism, and bilious temperament. To the extent that she made promises, her campaign consisted of appeals to particular interest and identity groups and of programs that read like the bullet points in a office memo and simply eluded the greater public.
She made little, if any, effort to speak to and allay the distrust the voters to whom Trump was appealing. They were a “basket of deplorables.” She and her campaign rested their hopes on the theory, popular among liberals, of a “rising American electorate of the young, minorities, and single woman. But her listless campaign failed to attract the same kind of support from the young and minorities that Obama had won in 2008 and 2012. In Iowa, she broke even among voters 18 to 29, and in Missouri lost them. And her vote among Hispanics fell six points short of Obama’s in 2012.
He also goes into how Trump won, which could be useful in defeating the Republicans in 2018.