You are ignoring the bandwidth differential of RF v Fiber-based transmission systems. We don't care if some random unknown crypto session happens on the internet - there is near infinite bandwidth - and someone is paying a bill (on both ends).

With amateur RF it is different - it is a shared, finite resource (in a given area/radius).

Not allowing enciphered communications is a fairly easy way to be able to audit what is taking up the spectrum. If it all goes enciphered, you have no idea what is occurring, for what purposes.