Car cover for winter?

[Jake]

That sounds like a pretty sketchy idea... let's try it on a car that doesn't have a brand new top, perhaps.

Matt, the top is designed to repel/deal with water and snow. I left my Miata uncovered in snow storms and plan on doing the same with the E36 'vert. If you're really concerned, get a fitted cover, but as Joey (and maybe others?) said, you typically want the car to be freshly washed when you put it on, otherwise it can move with the wind a bit and scratch your paint.