Hi! Welcome to the forum.
Well I use a pretty standard leather slip case from Amazon so my Desire is protected when it's coming in and out of pockets and such. When I want to dock it to my car it simple comes out of it's slip case and into the mount! The case then either sits on the passenger seat or in one of little pockets in the doorcards/dashboard.
I don't really see an issue with 'going naked' when it's securely docked in a car holder, nothing is going to come into contact with it so it should be fine. Although heres a funny little anecdote for you...
My mate had an iPhone, I think it was a 3G just after it came out. He was particularly pleased with his shiny new toy and so he bought one of those universal mobile phone holders to show it off on the dashboard when he was driving along. (Not that it was any use there, wasn't a sat nav or anything!) He used to mount this holder in the same place I do; on the right hand side of the wheel on the edge of the windscreen (I hate it being in the middle, gets in the way!) Anyway turns out it was off some dodgy market stall for a few quid... So one hot summers day we're driving along, me in the passenger seat, iPhone seated 'securely' on the dash and all the windows wide open.
We go round a particularly sharp corner that he took maybe a little too fast and the suction cup gives way, sending his shiny new phone and cheapo universal holder careering out the wide open window and clattering at some speed onto the road below!
Needless to say there wasn't an awful lot left of either the phone or the holder once they had been retrieved from the side of the road, probably having been run over a few times by passing cars.
The look on his face was priceless though, and well worth it from my point of view!
Moral(s) of that story?
1.) Don't buy cheap holders (and if you do, don't mount them next to open windows!)
2.) Owning an iPhone WILL bring you bad luck!