A virus is something that copies itself. If something is copying a virus, it is infected.

So the virus would have to infect both android and the cockpit to spread from phone to cockpit to phone.

Not at all, that's like saying floppy disk viruses happened because both PCs and floppy disks were vulnerable. Just imagine the cockpit to be a floppy disk. You plug your phone in, and your infected phone puts a file in the cockpit. Then someone with a vulnerable phone plugs into the cockpit, reads the file and is infected.

Not saying that's how it happened, just that it's possible.

The hole in the argument is, why would the second phone read the file and execute it? We are waaaay past autorun.

Why would the first phone read the file and execute it? ( this is an exercise for the reader, not an actual question )

Sadly, we're not: http://www.windows10update.com/2015/05/windows-10-tutorials-...