The headline is misleading. According to the story text, the floppy is used to load a new navigation database, which is important to be sure but not a critical software update.
By the 787 they were working to replace this all with code signing.
ETA: This bears repeating: aircraft have interlocks. There is a sensor that tells you that the plane is parked (wheels on ground) and there are connections, maintenance, and administrative changes that cannot be made unless this is the case.
Nobody is going replace the maps with Rick Astley somewhere over the Pacific at 3 am.