Akerosid,
I don't believe that Flybe has any interlining agreements still in existence. There is still a code-share agreement with Continental at Belfast, Bristol, Edinburgh, Glasgow and Manchester for flights to Newark, which is of little help to Channel Islanders.
I understand what you are saying about the lack of any inter-lining agreement with other airlines at CDG, specifically Air France, and it is somewhat inconvenient; the result of this will be that the majority of connecting traffic will still operate through London for British Airways flights or for other airlines. But Flybe will still be offering the islands' only service to a major international hub (Gatwick is limited in its choice of destinations) which is a whole lot more convenient than the bus or taxi from Gatwick to Heathrow. It is not perfect but I still think that there will be considerable connecting traffic using Flybe’s CDG service for this reason alone.
The tourist market is going to help sustain the flights as well, both from the islands to Paris and vise versa. Jersey Tourism does concentrate heavily on the French market, as does Guernsey, so the new route should be of benefit. Interestingly, I do wonder what the effect of the new CDG flight will have on the small Twin Jet operation to Orly. I’d imagine that this is primarily is a business niche route (looking at the prices) that Flybe will possibly undermine being a much cheaper and better marketed airline in comparison?