I guess that Flybe are being sensible with the new routes inherited from BACon. Flybe know full well that you can't operate the Embraer 145's with Q400 ticket prices. The likelihood is that the higher fares being charged by Flybe now are those required to make the aircraft pay for itself. You could argue that these fare levels are the ones BA should have been charging all along for these small expensive jets!.If exchanged for a Q400 in the months to come you no doubt will find more of the lower priced fares available given the operating cost benefit of this aircraft.
Out of Flybe and BACon, I know which Revenue Management team I'd trust to get the economics right!
Give it time, I think it's important to note how good the first month has been, yes there have been delays but the benchmark figure is departures within 15mins of STD and generally this performance has been remarkable. A friend in Flybe commented that they have acheived just over 80% punctuality in April for the entire operation. That's pretty significant when you see what was done in such a short time.
Every substitution of an E145 with a Q400 brings with it cost savings and this will be replicated through into lower fares for passengers, and better service given that Flybe know this aircraft very well indeed.