Carmen Ghia:

Because Trump did not campaign or spend money in the two biggest states: California and New York.  The Trump campaign conceded these states to Clinton with the result that the Republican voter turnout in those states was low.  If Trump were campaigning for the popular vote he would have campaigned in those 2 states and spent more money there.

Trump didn't spend any time or money in California and he still got 32% of the vote. In New York he got 37%.  If Trump had decided to campaign in those 2 states he would received a lot more votes and won the popular vote easily.