Obviously, the best idea is to use a bike cover. The trick is to find one that fits and won't come apart from the wind at highway speeds.
Keep in mind that most of an e-bike is weather resistant. Sometimes, all you need to do is cover certain parts.
I use these silicone stretch covers on sensitive electrical components:
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They can even be used to keep your saddle dry:
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They also work well to cover the opening on bikes with rear rack batteries:
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For down tube openings, as
@Mike-V suggested, I cover with plastic wrap and use an ace bandage to hold it in place.
Protecting your bar ends is easy with these waterproof arm protector sleeves:
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If you remove your saddle & seatpost when transporting, don't forget to cover the open end of the seat tube:
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