Now, i didn't get to see the programme and don't have Sky so probably won't get to in the future...but that won't stop me passing comment.
I would back what PhilH says. I work for a company that was on the receiving end of a similar investigation. It is amazing how by taking something out of context and applying some gentle spin you make it look far, far worse.
That said, I've flown FR a grand total of twice and that was plenty. I prefer being treated as a human.