They are cheaper because you don't pay the carrier / fuel surcharges or airport fees and taxes - you are only paying the base fare*. The only 'loss' BA suffers is not getting the carrier surcharge off you.
* though there is a minimum amount but I can't recall what it is at the moment though £300 rings a bell on long haul
BA knows what it is doing. It has a whole department looking at revenue management and it wouldn't be offering comfort seats unless it was profitable to them.