Oh, that's simple: healthy foods are more expensive, and don't have corporate sponsorship. Bear with me:
Most school districts use a third-party service to run their lunch rooms. Those services sign contracts, saying they'll feed the students for XX dollars per year. From there, they squeeze the most profit they can from the difference between the food they purchase, and the amount they're paid.
So, kids are getting the cheapest foods available. Sometimes, that's done by buying lower grades of food. Sometimes, it's by getting a kickback from big corporations, to only make their brand of sodas or chips available to students---because the brands we eat as children are the ones we are most likely to buy for the rest of our lives.
School lunches are all about corporate profits. Now that the nutritional guidelines that have been in place for the past few years are gone, there's nothing that says kids will get anything healthy to eat.