Actually, this makes some sense.
Mini DisplayPort is smaller than USB, and already rumored destined for the next iPad. This combination allows the iPad to integrate Apple's implementation of LightPeak as well for no additional space taken up on the device.
Consider also that Apple wants to continue to push the Mini DisplayPort as an 'industry-standard' connector. By being first to commercially implement LightPeak, perhaps they think this will make it easier to push both new technologies.
Imagine future monitors, both Cinema Displays and industry-wide, beginning to implement MDP for video and Light Peak, with I/O hubs in the bezel. It's a one-cable video/I/O connection for both laptops & iPads, in a minimally small connector. Sound like Apple much?