Simply, because, for most people, iTunes is easier. Doesn't require use of the filesystem, and, since iOS 5, doesn't even require you to plug it in to the computer since iTunes can now sync over wi-fi. So, even simpler than plug 'n' play.
And, regarding the connector, micro-USB is just for data and power - the dock connector also has dedicated lines for carrying audio and video, so it can do everything through one port - one of the reasons why audio docks are ubiquitous for iDevices. There is a micro-USB adapter that's going to ship with all European iPhone 5s, to comply with the European directive to have a single standard for mobile chargers.