Using VPN's networks can be isolated on the same media.
Even classified information is transferred this way over the Internet by Governments when the National Networks are unavailable or cannot reach certain areas.
VLANs, together with firewalls, can indeed be used to segrate multiple network on the same cabling media, and this is more than enough for most company networks and low level "classified" data.
But note that all but the lowest level "classified" data CANNOT be shared on the same cabling backbone - they must be physically separated. In fact standard ethernet cable is in most cases not good enough due to possibilities of wire taps and signal leakage - fibre optic is therefore the defacto standard. And "classified" data is not transferred over the Internet as a rule. Low level data may be securely transferred if heavily encrypted, but anything more restricted cannot go via the Internet at all.
The simple fact is, if two networks are sharing the same backbone, there is a real risk of comprising the security separating the two. The only accepted way to guarantee proper segregation is physical separation.
The articles don't really elaborate on the extent of the cross connection - I'd certainly hope the fly-by-wire system is independant! - but surely with a blank paper design, building in a real risk that the passenger network may affect any part of the flight system network is unacceptable.