Well, it cost more to design and build.
I personally would consider the total cost of dropping two atomic bombs much higher, for hopefully obvious reasons.
EDIT: Although, per the article, I might have been wrong about that:
> The loss of life was shocking. The B-29 raid on Tokyo on the night of 9 March 1945 is thought to have killed as many as 100,000 people, making it more destructive than either of the atomic bombs that were to follow.
Fascinating bit of history though, thank you for sharing.