If you plug in an MDP monitor to the thunderbolt port it doesn't pass the thunderbolt signals on down the line (and MDP monitors do not have MDP ports on themselves).
You can put an MDP monitor on the end of a chain though - eg, a Pegasus RAID box connected to the mac, and then a MDP monitor connected to the second port on the Pegasus.
The new iMacs have two thunderbolt ports for this reason - you can start two chains, or just have two devices without a hub (eg, two thunderbolt devices that only have one port each on them).