First of all, not all of the votes are counted. Even here in California, there are still absentee and provisional votes that never were counted, and won't be.
But a person said it pretty clear this morning on the new regarding the Popular Vote vs the Electoral Vote. Say it is the World Series, and you have 7 games, and one team wins only 3 games, but scores 50 runs, while the other team only scores 40 runs, should the team that scored 50 runs win?