Just my 2p on why you may have been rejected from the BA Cityflyer scheme whilst applying for Flybe:
I applied for the TCX scheme and attended the FTE Jerez assessment. I think they only took forward 32 people who had applied to the FTE assessment and thus just getting to that stage is pretty competitive. If you've been selected for the FTE assessment as part of the Flybe scheme then they won't also put you forward for the same selection process but for BACF - the assessment will be exactly the same for the two schemes apart from a bit in the interview which will be specific to the airline.
tl;dr: no point in getting people to do the same assessment twice
It definitely isn't due to them not being interested in candidates who have applied for other schemes though as FTE will keep your assessment results for 6 months and if you apply to another scheme will just use those (old) results in deciding whether to take you forward to the airline interview. I guess this may not be possible from Flybe to BACF due to the timings of selections though?
Good luck