I just arranged my own travel and accommodation when I travelled around Uzbekistan. Classic route would involve flying to Khiva from Tashkent and then making your way back by car via Bukhara and Samarkand. Hotels are dirt cheap as is car hire with driver e.g. the car journey from Khiva to Bukhara with driver took about 8 hours but cost only US$70 (that's for the car/driver, not per person). You'll also have the flexibility to take time to see a few towns as side trips if you so wish. You'll see some great sights. Only negatives are lack of restaurants everywhere and too few hotels in Tashkent if there's some event on in town.

Amanda, I found a site that is really much better than yours for anyone traveling to Uzbekistan. It is called East-Site Travel. They know much more about this region, having one of their offices right there (another in the States) and their tour prices are one of the lowest and are all inclusive. Plus, they do not use any third party service providers, which gives them more control over the details of your tour, like drivers etc. They are the nicest opeople to talk to and have lots of good suggestions. Also, they are happy to customize the tour to include some things different you may want to do.