The 'fly shuttle' service is just a clever marketing ploy to hide the fact you have 2or3 30 minute connections included in your ticket price. Don't you also need to clear UK customs at the first point of arrival, so all JER pax will have to disembark at SOU and re board?
After doing the trip once I don't see many PAX booking it again - especially business pax who this concept is aimed at.
Flybe pockets are not 'empty' by any means, however coming off the back of years of loses, and at times pretty big ones, one year of profit doesn't mean they are back on their feet yet. A conflict in Iraq and higher oil prices is the last thing they need and I also understand an impeding holiday pay law suit may need to be paid out soon?