He added that customers need to be aware that what they see as the lowest fare on a price comparison search may not wind up being the cheapest option once the fees are tallied.

"It's not transparent until you've gotten a certain depth into the booking: 'Oh, here's the seat selection fee. Oh, here's the baggage fee. Oh, here's the carry-on fee.' And watch out if you don't check-in online, there's a massive penalty if you don't," Vanderlubbe said.