You might want to make scripts in commandline.
You might want to make a script that would process several hundred books automatically.
You might want to make your own solution and you just use certain parts of software, just like Kovid (Calibre author) used many parts made by third party.
You might want to specify some very specific commandline options to the conversion utilities.
You might want to help somebody remotely, because he needs to convert some files or something, and instead of describing what to click, and what to expect, you just tell him: take this text paste it into commandline and it will do what you want.
You might want to solve a problem, so you run the commandline and see the debug information, instead of just program crashing and main window silently disappearing.
It is much better way to create several components that work independently and create an user interface that uses those components, than creating one big executable file. Unix systems do it this way.
Calibre was, at the very beginning, called libprs500. It was a commandline tool build by a very clever hacker, so he could access files on his Sony Reader PRS-500 from Linux.
Just recently somebody came to our forum asking how to convert thousands of free erotica stories for download in several e-book formats. He used commandline Calibre tools to make a batch conversion.
Several big-shot ebook publishers use Calibre to create (convert) their ebooks to various formats, from what I heard.