I think this discussion is geared a lot more towards the Upper Midwest, not the South as a whole. As many are saying, the climate of discrimination is very different between the two.
As a suspicion based on what little information is contained in the article, I'd bet that they were messing with ACARS to some degree. This is something you could easily do with off-the-shelf SDR hardware, and the protocol itself has no inherent security features.
As other posters have noted, this could mess with FMS flight plans as well as other logistics (which could be significant from an operational standpoint), but for actual safety of flight it's probably a non-issue.