The votes are still being counted, but it now seems almost certain that more Americans voted for Hillary Clinton than voted for Donald Trump.
The same thing happened in the 2000 election. Al Gore received more votes nationwide than George W. Bush. Two out of the last three Republican victories were with a minority of the votes!
Until and unless the Electoral College is abolished, this is likely to happen again, and always in favor of the Republicans.
The reason is that Americans do not vote directly for President, but for members of the Electoral College, who then choose a President, and that the Electoral College is tilted in favor of small states—most of them rural states with Republican majorities.
Each state gets a number of electoral votes equal to its representation in the House of Representatives, which is apportioned according to population, plus its representation in the Senate, which is two per state.
Democrats are concentrated in cities and in large states with large cities. Republicans are more spread out across the country, and are more over-represented in the Senate and in the Electoral College (and also in the House of Representatives, due to gerrymandering).
In American history, there have been four previous Presidential elections in which the loser got more votes than the winner. The losers were Andrew Jackson in 1824, Samuel J. Tilden in 1876, Grover Cleveland in 1888 and Al Gore in 2000—interestingly, all Democrats.
Jackson and Tilden were special cases. Jackson got the most popular votes and electoral votes in a four-candidate race, but far short of a majority. As provided in the Constitution, the decision went to the House of Representatives, which had to choose among the three top vote-getters. Henry Clay, who was third, asked his supporters to back John Quincy Adams, who was second, and Adams became President.
In the 1876 election, both Democrats and Republicans claimed to have carried South Carolina, Florida and Louisiana. Congress named a commission to resolve the issue, and an informal deal was struck to award the votes to the Republican in return for withdrawal of federal troops from the South and the end of Reconstruction.
Cleveland was like Al Gore and Hillary Clinton. He clearly won the popular vote, by a bigger margin than either of them did, and he clearly lost the electoral vote to Republican Benjamin Harrison. He previously had been elected President in 1884, and he went on to win re-election in 1892.
In 2000, many people in the Bush campaign expected George W. Bush to win the popular vote and Al Gore to win the electoral vote. They planned nationwide protests to demand that the results of the election be overturned. But the opposite happened. Gore won the popular vote nationwide, lost the electoral vote and conceded.
I think it is likely, based on Donald Trump’s statements, that he and his supporters would not have accepted the legitimacy of a Clinton victory if it had been him who won the popular vote and her who won the electoral vote. But Clinton, like Gore, recognized the legitimacy of the Electoral College.
The Electoral College is based on the belief that the United States is a union of sovereign states and not a union of sovereign citizens.
Replacing the Electoral College with a popular vote would be more democratic. It would mean that Presidential candidates would have to be equally concerned with voters in all states, and not just voters in a few states that could swing either way.
But abolishing the Electoral College would require a Constitutional amendment, and amending the Constitution requires super-majorities that are—rightly—hard to muster. Another proposal is for large states to mandate that their electors vote for whoever won the popular vote nationwide, provided that there are enough states with similar laws to determine the outcome of election.
Hillary Clinton lost the election, but is winning the popular vote by Tom Kludt for CNN.
It Isn’t Just Donald Trump: The Bush Campaign Plotted to Reject Election Results in 2000 by Jon Schwartz for The Intercept.