There are states, countries, and counties for a reason. The idea is that a smaller, more local government will serve its people better than a world government.
Lets say each country votes in the United Nation based on population. Lets say big countries like China and India's votes are so strong, that smaller countries like Sweden stand absolutely no chance in getting their voices heard. This system is unfair, because large countries with large populations with dictate how smaller countries should be governed.
Similarly, each state has some local power not based on population, but based on seats. This ensures that even if many people in the state die out due to a plague, or if there is mass emigration, the state does not lose all its power in having a say in their own interest.
Imagine candidate #1 winning every single state by a difference of 1 vote each. Candidate #2 only wins 1 state, but by 55 votes. If we decide the election with the popular vote, candidate #2 will win, despite having lost all but 1 state.
Lets say that a huge plague wipes out 95% of the citizens in California. Should California lose 95% their right to decide on national issues?
If we decide by popular vote, then politicians will put all their political programs, promises, and policies on areas with most density. For example, politicians will focus on cities, rather than rural areas. They will focus on New York, rather than Alaska. The politicians will not bother to make any changes or listen to areas with low population density. Why should politician put any funds towards Alaska if it doesn't give them any substantial votes?
Worse case scenario, the politicians will actually TAKE AWAY from underpopulated areas to give to populated areas. Giving every state a sizable influence in vote forces politicians to address the needs of every state, not just the ones with the most people.
That's one of the reasons why Trump won. Clinton's policies serve the city well. "When the middle class prospers, America prospers." But there were a ton of people living in the sticks, who are not middle class, who feel that Hillary's promise of the budding middle class does little to relieve them from the harsh life in the middle of nowhere.
This election was a testament to the success of our democracy. Virtually all the cities voted for Hillary Clinton. But our voting process gives power to all areas, including the rural areas. The sparsely populated areas of the rural lands was able to outvote and defeat the densely populated areas of the cities, because America gives power to everyone, every area, so that no area will be left unheard.
City folk shouldn't have all the say in dictating what the rural folk get. Just because the city has more people doesn't mean that rural folk don't matter. This is why voting by AREA is so important.