If it's just for towns, then wouldn't a nice, happy heavily-cottaged region suddenly be reduced to terrible famine by the sudden maturation of its cottages? It makes towns seem a bad thing. Who would want to exchange the food-neutrality of a grassland site for 1-2 extra commerce?
If it were for all the cottage-lineage, I could understand that as urbanization displacing farmland. It would however severely curtail the efficacy of using cottages to generate commers; you'd need a farm for every cottage you have, making them like commerce-mines more than anything else. This could have interesting effects on the game, slowing research by increasing the price of commerce generation. Natural sources of commerce would become even more important (rivers, luxuries). It would be interesting to say the least. Maybe not bad.
Perhaps my doom and gloom assessment of the Town's food penalty might be misplaced. It will be rare that many towns will mature within a short span. In fact, by the very nature of city-growth and worker construction abilities, maturation is almost invariably staggered. This would get you some time to start building farmlands to compensate. Still, I don't like that for the simple reason that it makes towns worse than villages. Your lucrative cash-center begins to rot over time...
If you decide to keep the implementation of food-penalties for any of the cottage-lineage, I think that it should be done for all of them, not just towns. Further, to compensate for the increased expense (in food) associated with cottage-commerce, I think that their commerce yields should be raised. Maybe not doubled, but perhaps a 50% increase? That might be difficult though, due to rounding.
Alternately, instead of assessing a direct food-penalty to Towns and their ilk, how about just make them mild generators of unhealth? Fundamentally, unhealth is just a miniature food-cost, and you could assign the development penalties with more finesse this way. Furthermore, unhealth associated with urban sprawl fits it just fine thematicly, doesn't it? The only issue is that you may have to tweak-up some of the health-providing options to compensate for the new unaccounted-for influx of filth and vermin.