Many people use fabric bedding simply because it's safer and much nicer to use. It doesn't harbor mites, it's not dusty and there's no way a hedgehog can get slivers in their sensitive areas. It's also relatively inexpensive after the first purchase, because all you have to do is wash it and it's as good as new. For hedgehogs with respiratory illnesses, fabric liners are great because they won't irritate the nose with dust.
All around, liners are just more health and eco friendly for the little quill balls.