In short, the Zerg faction is picked by players far less than the Terran and Protoss sides. Blizzard states, "We don't want to have a huge chunk of zerg players sitting somewhere further down, unable to rise through the ranks." In actual matches between factions, the Protoss side wins a lot more competing with Terrans in some leagues. Blizzard states that it is "working on solutions" for this issue.
Gallery: StarCraft 2 Screenshots