For the purposes of this article we define "natural" foods and meds to be ones that our ancestors consumed during the past few millions of years.
If our ancestors ate them safely, it is unlikely that they would harm us.
No one claims that all that occurs in nature is good to eat - we can think of many counter-examples, e.g. hemlock and poisonous mushrooms.
There are dangers in any source of substances that were not consumed by our hunter gatherer ancestors. There are many such substances in modern supermarket food.
Genetically engineered foods
Pesticides, herbicides, fungicides
Patented pharmaceutical products
Hydrogenated vegetable oil
Certain foods in excessive amounts, e.g. grains, sugar, fructose.
Until about 10,000 years ago, our ancestors were hunter-gatherers, consuming foods that were available in the wild.
Those who were unharmed by the wild plants of that time survived. Those who were poisoned by them died. Of course, we are descended from the people who survived. Therefore we can eat their type of food safely too.
Of course, we cannot obtain exactly the foods that were eaten by our hunter-gatherer ancestors, but we do not need to do that for the following reason.
Selective breeding by farmers, seed companies etc. has led to the development of new varieties of our food plants. But the methods used (e.g. saving seeds only from the healthiest plants, F1 hybrids, and even the recently developed "marker assisted selection") just bring around the same old genes in different combinations. Our metabolism still copes well with those genes. Therefore, varieties of the stone age plants developed by those methods are safe for us to eat. For example we can safely eat modern varieties of cabbage, even though the wild mediterranean sea cabbages from which they were bred were very different.
The most dangerous of the above are foods developed by genetic engineering. Far from bringing around the same old harmless genes in new combinations, as occurs with traditional methods of variety development and marker assisted selection, the processes used are highly destructive, causing random and unpredictable mutations in the genes themselves. It is very dangerous.
Another reason for natural foods being healthier is that they generally have a higher ratio of nutrients (e.g. vitamins, minerals, antioxidants) to calories than many of our modern manufactured foodstuffs such as sugar and wheat flour. Further, those nutrients tend to be present in the combinations that our stone age metabolism evolved to deal with. But that is a small effect in comparison with the dangers of genetic engineering.
The real reason that genetically modified foods can damage your health
It's not what most people think.