Pitotheat,
What is the relevance of the charters in your apparent argument that the Q400 is inferior as a low cost a/c to a 737. Yes, the EMA-VRN and NCL-SZG have airborne times of approximately 2hrs 30mins, but they are operated on behalf of a charter company, and if that company feels that the route is viable on the Q400 it is nothing to do with Flybe, they simply provide the service requested by the charterer.
Of the schedules you mention (and if you check my post you will note that I referred to current routes), only the BHX-BGY-BHX had airborne times of over 2 hours, and despite the proliferation of low cost airlines operating into BGY from the UK (not to mention BA on BHX-MXP) there was never any lack of passengers when the Q400 was on the route. So maybe, as has been suggested before on these forums it is not the majority of passengers who are against turbo-props, but the pilots.
Regarding drift down, MSA etc, only on the BGY and VRN routes could that be a problem, as operating North of the Alps/Pyrenees on the other routes the highest terrain is only about 5000' over the Massif Centrale (sorry if that's spelt wrongly). However you were surely aware of that. As for the weather, storm tops over the Alps/Pyrenees often reach above 40,000 feet, so any aircraft descending into, or climbing out of, airfields in Northern Italy may find problems with weather.
If any non pilots are reading this and should somehow get the impression from your post that the operation is unsafe (surely that wasn't your intention), I believe that at least one CAA flight ops inspector is current on the a/c, flies it several days a month and is well aware of the operation of the Q400 over the Alps and would presumably have objected if the CAA thought it was a problem.