Yes, absolutely duffel bags can be put onto an aeroplane as checked luggage in the cargo hold. You may want to invest in some padlocks to make sure it's extra safe, however.
Your duffel bag can potentially be taken onboard the aircraft as a carry-on too, as long as the size of your duffel bag is within the airline's requirements for carry-on luggage. Generally, this means it should be no larger than 9 inches x 14 inches x 22 inches. Most brands make a travel duffel bag that'll specify it meets carry-on size requirements.