"Air gapped" means that there is a physical separation between two networks (i.e., there's "air" between them). If two networks are physically connected, there is always a chance that someone could bypass any software security restrictions. If the two networks aren't physically connected, there's no way to gain access to one network from another.

In this instance, the inflight entertainment network and the avionics network were physically connected, and the security researcher was able to gain access to the avionics network by connecting to the inflight entertainment network.