It seems I was misread. I never said they never produce profits. I used to usually get profits. I was just stating I was not getting any lately, out of the last 5 or so.
You invest wherever you want. If your goal is to boost production over 100%, cities are your best bet I'd say. If you just want to bring it to 100%, then depends on you.
I've invested in rurals and townslands with suboptimal production levels in order to increase their food output, to make sure I had a steady supply from them, while helping them out a little extra. I wouldn't have done it if their production was at 100%, though.
Speaking of which... WHY won't food production go over 100%?
Because food is a resource. You can't just put more money in and get back more apples than exist in the world, maximum food production is just that, maximum food production.