as long as you are bagging your skis and checking them for the flight, i'm sure you will be fine. i've been flying my skis out when i come to school in CA and i haven't had any problems. I was covering the tips and the bindings with cardboard and then bagging them but the last trip i just put them in a ski bag (which is nothing fancy, no real padding, just a zippered ski bag) and they were fine. skis are meant to take a beating and they will more than likely take it worse on the mountain then they wouldbeing checked for a flight.
if the issue is you don't have a bag and that's why you are using bubble wrap and/or towels...you'll be col with that too. wrap will cover up your skis and keep them together...and it will prolly protect them from getting scuffed and scratched (if that's something you are worrying about). all in all, skis are built (or should be built) to hold up on the mountain and they should hold up fine when you're flying.