Multani:
I guess it's just the whole "mind games" aspect of blue decks that make them firstly, an annoyance to play against, and secondly, very frustrating to lose to. A well-tuned blue deck can stop all the serious cards from hitting the table, and the prospect of always asking "are you going to counter that?" makes blue a major annoyance, and losing to blue, especially at the hands of some card like Morphling or Mahamoti Djinn (in the old days) is frustrating because of the fact that, if the blue deck is played right, there will be many turns where the opponent won't be able to do anything useful.
The fact that blue isn't too good at multiplayer also seems to raise a big question as to why blue is so many people's favorite color. Multiplayer seems to be a foundation of casual play, and blue is definitely a "non-casual" color, so that's an interesting commentary on the position of the people who voted on the topic.
Y The Alien:
How can you say that blue is saving Magic from combo decks when it finds its way into so many combo decks? Extended was ruined this past season because of Donate and Illusions of Grandeur (or was it Delusions of Mediocrity?), and not too long ago, there were tons of mana engine decks that focused on Stroke of Genius as its kill card (which never made sense in a real-life setting; I get a stroke of genius, and I die?). Let's not forget Turbo-Stasis of a couple years back, either. Blue has been a focal point of combos and combo decks for a long time, all the way back to the beginning, when Mana Drain/Mahamoti Djinn was popular.
As for the idea that blue beats everything else if played properly, that is probably the reason why people don't like blue. In a game where no one color is supposed to be able to beat everything else, blue finds that it can, if played properly. Green can't win against everything, as its creature-heavy strategy loses to dedicated control (blue or black). White is strong, but it loses out to faster strategies or land denial(green, black or red). Red is good at resource denial and some speed, but some strategies don't require too much land, and control can slow it down considerably (green and blue). Black's combos are fast, but there is still the ability for other dedicated decks to overrun those combos (green and white). Blue, on the other hand, while it has its weaknesses, has the all-powerful answer, "I'll counter that." Sure, you can't counter everything, but if you counter the four creatures your opponent had in his opening hand, why would you need to counter Wild Might or Vitalizing Wind? What you called the "moderator" actually is the first sign of dominance of blue. The fact that it can beat anything if played correctly demonstrates its unfairness.
I don't hate blue (I'm making a blue deck right now, as a matter of fact), but I think it's very easy to see why so many people at least dislike blue, and I'm also very shocked to see blue with so many supporters for favorite Magic color.