I've only flown FlyBe once, but I was NOT impressed. In addition to the charges already mentioned, if you opt to check in online and print your boarding pass and, heaven forbid, lose it, they charge you something like £10 to print a new one.
Plus I got an idiot person at check-in who didn't see that my bag was prepaid, pinched my boarding pass, stuck a sticker on my passport and told me to go over to the ticket desk where they would give me a new one. So the guy at the ticket desk tried to charge me again for my bag. But at least he was nice when I explained the situation, and printed me a new boarding pass, without charging me for it. Of course all of this was at 5.30 in the morning when I'm not a happy camper anyway!