bike cover for bike rack

Anybody use a bike cover for your bike racks on your vehicles? I just bought a Topeak race bike cover, and have a couple quaries with it:

1. It's not really designed for bikes with aerobars as far as I can tell, maybe I'm just putting it on incorrectly!?

2. With my bike rack, I'm gonna need to cut a hole in the top to allow the bike rack to clamp onto the bike. That kinda sucks!

Anybody have experience with these or know better ways to protect your ride when on the road?