In research, we have a saying: Cheap, Fast, or Right. Pick any two.
It's like that for food: Cheap, Fast, or Healty. Pick any two.
Healthy food tends to be more perishable, which I think is a big part of the problem.
If you want to be fast and healthy (i.e. high-quality perishable food), you have to prep the veggies and bake bread on-site like Panera Bread. But this is a little more expensive and it limits your menu to soup/sandwich/pastry/coffee (i.e. Yuppie Fast Food).
If you want to be cheap and fast, like McD, BK, Arby's etc, you have to pre-prep your food at a central facility and ship it to the outlet store. But then the food has to be able to survive cheap transport, so it has to be made of non-perishable stuff like potatoes* or fat, or frozen like meat, or full of preservitives. If you design your food for transport, the food is no longer healthy. And the super-cheapie restaurants cut quality even more to stay cheap, and add grease to make it palatable. No amount of exercise can make up for low-quality meat or preservatives.
If you want to be cheap and healthy, you have to stay home and make the food yourself, which takes lots of time and effort.
I really have to give credit here to Subway. They are the only ones who are able to be cheap, fast, and healthy. But they have to limit their menu to stuff that transports well, like cold-cuts.
By the way, don't most of these restaurants make most of their profit on soda? In college I ate a lot of Taco Bell.

I'm sure that even the crappiest food didn't cost much less than what they charged, but I do know that they charged $1.39 for a nickel's worth of soda.
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*I heard that at the end of Supersize me, they show a box of French Fries that doesn't decompose for something like -- 6 weeks?