I don't think any citizen's vote should count more than another just because they're part of a minority, geographic or otherwise. Imagine the uproar that would ensue if a politician suggested that a racial, ethnic, or religious minority group would have their votes count for more.
I am more split on the issue. geographical votes result that problems and needs in one area don't get overlook because of population statistics. In the worst case this could lead to countries splitting up into smaller parts, just so that each area which its own special problems and needs can govern themselves.
To take a practical example, the European parliament. Seats are allocated to each state according to population using degressive proportionality, which mean that Luxembourgish voters have roughly 10x more influence per voter than citizens of the six large countries. The alternative would be that Luxembourgish have practically no vote, since their population would be too small to even get a single seat, meaning their vote would have 0 influence. Which one is more fair?
I agree with you about the European parliament example, but speaking of the U.S. situation specifically, we already have a bicameral legislature with disproportionate representation for lower population states in one of its houses. We also have federal courts to step in when any laws are stepping on the rights of minority populations.
You've also touched on one of the longest-running debates in American politics: should we treat states as independent and semi-autonomous or allow the federal government to dictate policy direction for the nation. You can probably tell what side I'm on. People still claim that the American civil war was about the South defending "states' rights" when I, and many others, feel that it was about defending the rights of many people actually in those states.
That might be a little off topic. Anyway it's an interesting debate, but it's just hard to see how a candidate for national office can win more votes across the country and come out the loser.