I don't know why people have such a problem with the way Calibre stores its files. Like dwanthny said you have complete freedom as to how to export files if you want to.
Another thing is as I add books to Calibre I don't delete the books from their original format. I had my whole library backed up to bluray before I even started messing with this program when it was new to me. So I don't need to worry about losing anything.
Once I complete adding all my books to Calibre I will back up my library (including the Calibre database) one more time before I become completely dependent on Calibre and delete from my hard drive the original files.
If I decide someday in the future that I want to switch to another program I can export in a particular format or go back the original files that have been backed up. Complete flexibility.
Don't natter over the way Calibre works "under the hood". Just use it for what it does extremely well and don't worry about how it keeps the files organized.
iTunes and iPhoto are the same way. I don't have any control over how they organize the files internally either and don't care as long as I can get the files when I need them, convert them, or export them to transfer elsewhere.