Upvote:5
I have flown with many duffel bags as hold luggage and I have never had a problem with the handles. The warning you quote refers mostly to big rucksacks which have thick loose shoulder straps, and maybe even chest and waist straps.
Having said this, if you want to be extra careful with your luggage there are a few options you can consider:
Wrap your luggage in plastic, either at home or using one of the many wrapping services in the airport
Tie the handles together by wrapping them with tape, or use zip ties to hold them together