"WTF are you doing to your CDs that causes the packaging to get "thrashed"? "
carrying them in bike bags, cars, and other places where they can be exposed to water or other spilled liquids, or to friction/abrasion from other objects; setting/stacking/placing them on work surfaces where stuff gets spilled; carrying them from indoors to outdoors, where they can get dropped, etc.; in other words, normal use outside of from-the-shelf-to-the-stereo-and-back. that lovely, hand-watercolored Windy & Carl paper sleeve doesn't look so good when it's sitting in a coffee puddle on your computer table, and bad things will happen to that copy of "Year of the Horse" when you get caught in a shower cycling home from work.
cardboard covers are a limited-life-span cover for a purportedly unlimited-life-span disc (yeah, yeah, let's not get into the CD deterioration thing now, please) and as such are inherently inefficient. they scratch the discs, they split at the seams over time and no longer perform their assigned function (unless they're the type that have the panel with clips that's made of, OMG,
plastic 
) [e.g. i had to cello-tape my copy of "Lift Your Skinny Fists..." together within six months of purchase, and i wasn't abusing it, either, just taking it with me on the train], and the act of sliding them in/out of shelves wears the graphics/printing off the surfaces. cardboard covers are an inferior storage medium in every way to jewel cases other than the space they take up and the relative fragility of the cases, which could be solved quite simply with a different compound. my concern for the environment compromises at the precise point that the utility of the thing i'm using is negatively affected. cardboard cases...i say the hell with 'em.