CNN has a nice article that lays out 24 theories. These boils down to three main themes, however:
One: Democrats backed Clinton despite Sanders being a stronger candidate, and then Clinton couldn't unite and mobilize the party. Many strong Democratic candidates didn't run.
3. Because of low voter turnout
10. Because the Democratic Party establishment didn't push Bernie Sanders
12. Not because of millennials
13. Because of Gary Johnson and Jill Stein
20. Because Democrats focused more on turning out supporters than growing the base
21. Because the Democratic National Committee selected the less competitive candidate
24. Not because of Comey
Two: Voters were deceived by lies, blinded by fluff and inflamed by a demagogue.
1. He won because of Facebook and its inability or unwillingness to crack down on fake news
2. Because of social media, generally
4. Because celebrity outlasts substance
7. Because of Russia after all?
9. Because rural Midwesterners don't get out of the house enough
23. Because of Comey
Three: Democrats ignored the white working class sense that the media and system are corrupt and they don't matter and Democrats didn't consider their racist concerns legitimate
5. Because of white women
6. Because of white male resentment
8. Because the left and coastal elites shamed Trump supporters
11. Because Reagan Democrats surged in Michigan and Midwest
14. Because political correctness set off a nasty backlash
15. Because he simply listened to the American people
16. Because college educated Americans are out of touch
17. Because Americans are biased -- but not against any race, ethnicity or gender
18. Because voters believed the system was corrupt
19. Because he remembered 'forgotten men, women' of America
22. Not because of racism
Too Many Democrats Stayed HomeTurnout (voting-eligible population):
Steve Greene highlights much lower turnout by supporters of Hillary Clinton than by supporters of Barack Obama, than in either 2008 or 2012, while Republican turnout has been more or less static. Clinton won the popular vote, but by a margin much smaller than Obama in 2008 or 2012.
Note that Hillary Clinton didn't need to perform nearly as well as she was polling prior to the election to win. All she needed to do was perform 1.1 percentage points better in Wisconsin, 0.4 percentage points better in Michigan, and 1.3 percentage points better in Pennsylvania. That is all she needed to win those states, even though that would still have been far worse than she polled in those states.
Sanders won in the primary in Minnesota, Wisconsin, Michigan, New Hampshire and Maine, which are all relatively close states where Clinton underperformed in the general election, although Clinton did win Pennsylvania in the primary against Sanders.
But, it could also have something to do with overconfidence inspired by inaccurate polls.
* The Electoral College has a Republican bias.
Because the Democratic party is more urban and the Republican party is more rural, a popular vote tie means an electoral vote win for Republicans. Democrats need to win by at least two or three percentage points in the popular vote in order to win the Electoral College. Hillary Clinton won the popular vote, but not by a big enough margin to defeat Trump.
* Republicans are more partisan than Democrats
This was a race with the two least popular major party nominees in history. But, Republicans didn't care and Democrats and unaffiliated voters did.
Ultimately, despite having the worse major party nominee in Republican party history, who was morally flawed, sexist, a serial rapist, a racist, a fraudster, and a man who has made many horrible, horrible business decisions, grass roots Republicans ultimately decided to overlook those flaws pointed out in the primary, because they want their party to win and support the "Alpha Male".
Democrats like a thin elite of Republicans, are choosier and didn't get as strongly behind their own flawed candidate who was not an "Alpha Female", who was not an inspiring orator or visionary, and who was unable to dispel criticisms from Democrats that she was a centrist corporate pawn and from Republicans that she was corrupt. A lack of enthusiasm from Democrats and unaffiliated voters for Clinton translated into lower turnout by supporters because they are pickier and hold their leaders to higher standards rather than blinding getting behind the cause.
* Clinton failed to inspire.
Clinton came up short in free media because she didn't give them the inspirational or at least noteworthy soundbites that make news. Without them, you don't get the coverage and hype that you need to penetrate to consciousness of the electorate.
The most inspiring slogan of her entire campaign, "a taco truck on every corner" was devised by a Republican critic and adopted by her supporters because she had nothing better to offer.
You can't win hearts and minds with twelve point plans and policy nuances. You need to communicate a vision emotionally and delegate the details to others. Without a short defining message to sum up her campaign in a few words, she let others define her in a negative light. Without opening up in her speeches, she couldn't communicate her heart and character to the American people. Presidents need to be hedgehogs and not foxes.
You can call those expectations male bias, but inspiring speeches are a Presidential candidate's stock in trade and a central part of the process. Without them, you can't win.
If you don't reassure the public with a constantly repeated message, they assume the worst and dwell on the negatives.
It wasn't that the public has deeply embraced the Republican vision for America. While Clinton's campaign did not deliver the coattails that had been expected, the Republican majority in the U.S. Senate narrowed from 54-46 to 52-48, and Democrats gains six more seats in the U.S. House at the expense of Republicans. Few incoming Presidents lose support in both houses of Congress in the year they are elected. Trump takes office after failing to win the popular vote and winning the Electoral College by a razor thin margin in three critical states.
But, Clinton's campaign was not rousing enough to surmount Trump's thin support, and failed to realize the coattails she could have commanded, and indeed was expected by polls to command.
* The media and political elites took too long to respond to big lies; they weren't effective
Only one major newspaper in the entire country, in Las Vegas, endorsed Trump, that paper had a personal connection and financial interest in Trump, and that endorsement wasn't enough to prevent Trump from losing in Nevada. Indeed, almost every state in which Trump has significant financial investments rejected him. His popularity fell following every general election debate.
The utter failure of this media consensus to have any meaningful impact on the outcome of the election is a profound statement about its irrelevance in modern Presidential politics.
Trump lied all day long, every day of his campaign, and the media and political elites didn't manage to start taking him seriously to task for this until the final month or so of the campaign after most people had already made up their minds. Somehow they could never made the fact that Trump was a liar or that his character, in general, was profoundly flawed stick, in large part because the political right has spent decades convincing itself that the mainstream media is biased and can't be trusted.
* Bad polling data led to bad tactical decisions
Clinton mounted a campaign tactically based on the assumption that the polls were accurate and that she had solid support in Pennsylvania and the Midwest, when in fact those states were far closer and needed far more attention. She made these decisions because the polling profession across the board failed to accurately capture the strength of Trump's support.