I have played about with Maptools and am very impressed with it, that said I found it to have a steep learning curve and troubleshooting conection issues could be a bitch. I would be quite willing to use but the people I wanted to get to use it would not touch it after that one session.
*Nods*
Maptool is powerful, don't get me wrong. But, as Ardoughter mentioned, it has a rather steep learning curve. The VT comes with next-to-seamless integration with the CB and VT. To get the same level of integration with Maptool requires the installation of frameworks and other stuff. In addition, you would need to either type in or use a macro to parse the monster/character data and bring it into Maptool.
The DDI VT is designed for 4E, as I mentioned above. All of the stuff it uses and how it works is optimized for a group playing 4E. Maptool, by its very nature, cannot, out of the gate, be optimized for any game system. It is system-agnostic so that you can customize it for your individual system of choice. Can you get it to be hyper-optimized for 4E (or any other game system)? Yes, yes you can. But the amount of work and effort that is required to do so is significant as compared to the amount of work required to get the VT optimized for 4E. For some people, that minimal effort (that you would be doing anyways when the players create characters and the DM makes his map/chooses monsters) is worth a monthly subscription fee.
As I mentioned above, Maptool rocks, but they are designed for two very, very different purposes. Each has its advantages and disadvantages.