I know that Walker's would provide a shower cap in a small plastic bag and ask that you put the cap over the control box if it was raining. However, I also heard that at least one of the rental companies said not to use it in the rain at all.
If I am out and it is raining, I will put a poncho on, draping the front over the handlebars and the back over the seat back. It generally works to keep me dry.
And basically I have no problem in the rain, except having to disassemble the unit to get it into my car quicky if I am done for the day at the parks (without getting completely soaked..