I think it was because Uther had all the dragons killed, but instead had the last dragon chained up. I think he had them killed because they were magic and he thought they were dangerous. I'm not sure why the last dragon wasn't killed.
I can't promise that's right, but it's what I remember!
Just to finish from chickencheese, the last dragon wasn't killed, but kept under the castle to serve as a reminder to all the people of Camelot and visitors that magic wasn't tollerated and that whoever practised magic would have grave punishment (quite literally).
