When I had the soft top replaced on my car I went to Babies R Us and bought the largest, softest baby blanket I could find. When I fold the top down, I tuck in in between the windows and then fold it under to protect the top from the bottom of the boot.

I sometimes get odd looks when I pull the top up and people see it's tucked in with a blanket that has teddy bears all over it, but I've never gotten a scratch on it. I occasionally toss it in the washer to make sure any dust gets washed out before it can scratch anything up.