In the beginning, I used Calibre to simply keep track of my ebooks (textbooks, science etc., PDFs mostly). Before Calibre, all of that was very chaotic. (Actually, I am looking for a good app for my movies, music and documents - they need some clear cataloguing system, too.) I also used Calibre book reader to read the few epub/mobi ebooks I had.
Now I have an ebook reader, and I have started reading some fiction ebooks, too. Using Calibre to transfer my ebooks to the reader was the most logical way to do that: I don't have any copies outside of Calibre and don't look into Calibre's blackbox

- so if I didn't use the transfer features I would have to save all the books I want to transfer first. In my case, I don't see any reason I should use something else than Calibre to transfer my books. I enjoyed Calibre a lot before getting an ebook reader and now I enjoy it even more

. (If only I could find such good apps for other kinds of data... - If anyone can recommend something, let me know!)