The difference is in their aggregate value. I know a lot of you guys don't believe in WAR but flawed as it is, it allows you to make a comparison between players, and importantly because it measures the players value in terms of runs created or runs prevented, it allows you to directly compare pitchers to position players. In 2010, Felix Hernandez was not clearly better than Josh Hamilton. In 2011, Verlander was on a level with Jose Bautista and Jacoby Ellsbury. Therefore a vote for Verlander for MVP was more defensible this year than a vote for Hernandez last year.
There's also the whole "he was on a winning team" thing, which probably helped Verlander quite a bit and penalized Bautista and Ellsbury, and by extension, also penalized Hernandez last year. The shiny 20+ win record looks nice too.
Never said the system was foolproof.