The Electoral College only affects the election of the President, who does not (despite popular misconception) actually run the government the way a CEO runs a country, rather he represents one of three equal and (ostensibly) separate branches of government. The Electoral College doesn't determine the distribution of representatives in Congress, nor the election of judges.

Obviously rural states would not cease to have a voice in government if the President were elected by popular vote - which is in essence what the Electoral College is designed to prevent - because most Presidents have been and yet rural states somehow persist, pass legislation and maintain political power.