When the rule came in, many years ago, there were exemptions for airlines who were already majority owned outside of the EU (2 UK airlines at that time spring to mind, Britannia Airways, which was 100% ownbed by the Thomson Corporation in Canada and Monarch Airlines which was 100% owned in Switzerland)
That ownership per permitted to continue (since they could force the business to find new owners) but if any ownership change was to occur subsequently then majority ownership had to be within the EU.
One would hope that for the UK based airlines, those similar rules are agreed as part of BREXIT. (and yes Thomas Cook is a UK PLC, therefore Condor for example is 100% owned by a UK parent currently. Of course what we don't know is the % of TCPLC shareholders who are EU based but not UK based, it may be they still ahve over 50% EU shareholding without any change.