I use a soft one, with padded wheel bags inside. Not had a problem - it has the relevant marking on the outside.
I always put spreading bars in when I take the wheels out - I always think this will protect the fork and rear triangle should it get weight on it. I made them out of some old carbon fibre tube (golf club handle I think) - take the skewers out when you remover the wheels, insert tubing, put them back on the frame.