Most being the operating word here. Economy class tickets still make a profit if the airline wants it, just see the vast majority of regional flights which have zero business class seats. Southwest for instance has single-class layouts.

Some airlines "take" the marginal economy seat loss on larger planes because those are the ones they can fill with business class seats and make an even larger profit.

Even then it's a complex math on whether economy is hurting those flights' profit margins since those people buy things in-flight such as Wi-Fi and extra bags. Base fare is not the only way airlines make money.