The reason that smaller states are slightly over represented is because of the rule that each state gets at least 1 house rep and 2 senators.It goes by population. In smaller states like North Dakota, Wyoming etc they have less people so the votes are done for every 140k citizens and they have about 3 votes. In bigger states with more electoral votes like new york its for every 500k people(can't have too many votes) and they have about 29 votes in total because of the volume of citizens living there. It's about as close as giving misinformed people the voice they thought they'd have without resorting to mob rule IMO.
The electoral college apportions votes to states based on congressional representation. So small states have 3 EV no matter what (1 rep, 2 sens.). If the EC was completely based on population alone, some states/territories (Alaska, DC etc.) would only get 1 EV.
This all goes back to the Southern states wanting a balance of power that does not favor the populous north. It really boils down to the existence of the senate, which represents all states equally - regardless of population.