I mean if you add everything up - land value, labour, food costs, etc - I'm fairly sure they're selling eggs at a net loss, however, it's not a capitalist endeavour unlike the industrial production. And IMO that is the key difference, that is, they produce for themselves and sell the excess and earn some money off of it, it's not their primary goal to do so.
OTOH for shop bought eggs you also have to add transport (fuel/truck maintenance), storage, commercial land rent/interest costs, electricity, and of course the mark-ups along the way by processors, distributors, and—most of all—the shops themselves, that use their monopoly powers to reduce the margins for everyone else. And if we're doing like-for-like, you have to buy certified 'Pasture Raised' eggs.
Or they're using "surplus" resources (like their backyard, and domestic food scraps) that they'd still have otherwise. Which is something that is not commercially scalable. Unless, I guess, someone tries "Uber but for chickens".