The entire story is bogus.
The systems are isolated just fine.
One of the collateral PDFs for the device shows it connected to "IFE (In-Flight Entertainment)" (http://www.teledyne-controls.com/pdf/NED_Brochure.pdf).
Just the existence of such a device gives me reasonable cause to believe that there's more interconnection than "isolated just fine". While I have a lot of respect for the engineering processes that go into aviation systems, I've also had enough practical experience in IT security to know that blind faith in things being done right is foolish.
[edit] I've seen the claim made more than once in this thread without a source. I understand that the article was probably very wrong. I'm just interested to know if a reputable publication has confirmed this or if it's just conjecture.
According to recent reports, the entertainment system is not fully isolated from the plane's navigation systems. However, Boeing has denied this.
http://www.cnn.com/2015/05/17/us/fbi-hacker-flight-computer-...