The map below shows who won the election, County by County. As you can see from the map, Hillary Clinton won a small number of counties throughout the country, compared to the number of counties that Donald Trump won, but Clinton still won the popular vote.
This is exactly the reason we have the Electoral College and not the popular vote to determine who the President will be. Otherwise, Los Angeles, Miami, New York City and Chicago would determine who the President is and there would be no reason for a candidate to campaign in any other cities or states. The Electoral College gives a vote to every state, no matter its population, so all Americans have a say in electing the President.