I've found Flybe quite a reasonable airline. All airlines, particularly the low cost airlines have hidden fees, such as for putting luggage in the hold, credit/debit car charges as well as charging for seat selection. Putting these things aside, they're quite a decent airline. The Dash 8 Q400's can be a bit noisey, especially between the props in rows 8-10, but that aside, they're quite sturdy, well built aircraft, so nothing to fear there. And the Embraer's are fantatsic aircraft to fly, spaceous legroom and large windows.
On occassions, a Flybe aircraft will have to divert due to low visibility conditions where as other airlines will have no problems landing, I can't remember the reasons, something possibly related to CAT approaches certification. I have only had to divert once due to this.
All in all, a respectable airline. I just wish they had a Jersey European retro aircraft