despite the replies, the real answer is a very simple "because there's more Alliance in queue than there are Horde".
So if you t hen asked "Why are there more Alliance than Horde?", that question is [partially] addressed in your responses. But a big part of that has nothing to do with gear. There will always be more Alliance than Horde because players "typically" roll something they can relate to....especially introverts. Its much easier to relate to a human than it is to a Tauren.
WoW has always been Alliance-heavy and always will be (imo)....which means Horde will always have shorter queues (and of course there will always be exceptions for some servers where specific player-types migrate to).