You can get speaker can covers just for those. I suppose there might also be tower wraps, but I've never seen one. I've heard of people using sheet plastic or even saran wrap when they are towing long distances - just wrap everything above the roof of the tow vehicle. Of course that could turn into a pain depending on how often you travel.

I've also read about using Pam cooking spray once the tower is clean to help prevent things from sticking... I can't remember if this found to be a dumb idea or genius - and I haven't tried it myself.