Fruit, nectar, or milk has been produced dilligently in a way that it's directly digestible.
For example, plants needs to bear fruit to sprout their seeds. The seeds doesn't want to be eaten, it wants to grow. The animals who eat the fruit help the plants to sow the seeds somewhere. Same applied for nectars.
On the other hand, milk is produced for newborn of the same species. That's why we still suffer from lactose intolerant because cow milk means to be consumed by cow, not us.
However, doesn't mean we can't eat other food. That's why we invent cooking.
The Modern Approach To Food Reduce The Value Of It
Fast food is convenience, however it is not only strip the nutrient, but also strip the social experience of eating the food.
GMO or other modified organism may be beneficial for us, but we don't know the effect of it in the long run.
Globalization has make any food available in any place possible, however this means local food are being replaced significantly. Unfortunately, our body can't adapt for change quickly. That's why some people can't digest certain foods.
Abundance of food in supermarket or restaurant make us eat more food than we need. This leads to "modern" diseases like obesity.