Is the connector the only difference between a Cinema Display and a Thunderbolt Display? Is the connector the only difference between a Cinema Display and a Thunderbolt Display, or are there other features that changed between the two models as well?
The Thunderbolt monitor includes a number of integrated peripherals as well as being a monitor:


Three powered USB 2.0 ports
FireWire 800 port
Gigabit Ethernet port
Thunderbolt port


The actual connector for MiniDisplayPort and Thunderbolt is the same, but Thunderbolt can pass many protocols over the same cable, not just A/V signals.