And the electoral college is the GOP. Is that your point?
The issue is that in races which involve more than two parties - it can happen, and indeed has happened fifteen times according to the above FEC pdf, that a person with a minority vote (less than 50%) wins. Clinton did not have the majority in 1992 or 1996.
More to the point, even in a two horse race it can happen. The example given in the above was a candidate (e.g. Palin) winning by a slim margin in many states while the opponent, the popular vote leader (e.g. Obama), wins by huge margins but in fewer states.