I've flown with a cardboard box on these routes
Jet2 Leeds to Rome
Ryanair Stansted to Bucharest
Wizzair Luton to Sofia
Flybe Berlin to Doncaster
Easyjet Geneva to Manchester
I've never had a problem - my bike has always been accepted without comment and has always arrived intact with no dents or scrapes. Using the box, you can fit all your luggage in there along with the bike and you can pad it out with as much bubblewrap/etc as you like. Also, it's free! All it costs is an extra hour to reassemble your bike at the other end - would you risk your bike for the sake of that? I & Miss B will be flying with bikes again this summer, with different start and end points, and will certainly be cardboard boxing it once again.