If we keep digging into the issue then at then end of it most probably is cost.
air interface security is a critical challenge to all radio protocols, not only Mavlink. In civil aviation the threaten are less as airplane does not rely on ground remote control and all main lines are in closed loop inside the plane. That been said, you can still easily hack into the UHF/VHF channels.
Radios on UAV started with low cost radios like 433/900 MHz, which you can find them widely used in wireless door bells, TV remotes, car remotes, etc. These radios are almost 'naked' in front of hackers, but you just do not notice them in daily life as that even not worth caring.
Comprehensive encryption techniques can be added into eventually, but that would require hardware upgrade at both ends of the remote control system, which will increase the cost for sure.
And for advanced radios like Wifi, protected under comprehensive encryption, and still have the chance to be broken into.
So for UAV radio security is more notable than other scenario as it relies on remote radio control. But if you would like a serious implementation that will go beyond the scope of hobby applications, mainly in sense of cost.