You can't really compare routes purely based on load factor or number of passengers carried.
The MAN-LDY may appear to be doing rather well LF wise, but no-one other than the commercial department at BE knows what the yield and is on this route.
Simple test - fare ranges on domestic routes (not very scientific but gives some idea how some routes generate a lot more revenue than others):
MAN-LDY tomorrow (Aug 18th) £65.03 one-way.
MAN-EXT tomorrow (Aug 18th) £109.52 one-way.
MAN-ABZ tomorrow (Aug 18th) £77.52 - £132.52 one-way.
MAN-SOU tomorrow (Aug 18th) £84.99 - £174.99 one-way.
MAN-NWI tomorrow (Aug 18th) £63.48 - £129.52 one-way.
MAN-EDI tomorrow (Aug 18th) £57.48 - £112.52 one-way.
Economy Plus is also another indicator, the top fare on MAN-LDY is £135.03 one-way whereas MAN-SOU is £199.99 one-way and MAN-BHD is £163.42.
Clearly BE's commercial department don't think they can charge quite as much for the LDY flights as other routes. It is a balancing act to attract as many pax as possible at the best possible fare. Charge too much, LF and revenue fall, charge too little, LF rises but revenue generated is not as high as it could/should be.
This is just the fare (inc tax) but also the amount of ancillary revenue generated from bags, seat selection, drinks & snacks etc. will also need to be included.
It could well be that MAN-LDY does OK on basic economy bookings but relatively few pax spend anything on the extras that really help make a flight profitable.
Bums on seats doesn't necessarily make a route a success.