Chickens can fly (just not very far). While there was never a time when chickens filled the skies, their ancestors were a bit more adept than current breeds.

Why did chickens evolve to not fly?

Because of select breeding, chickens have bigger pectoral muscles than junglefowls, decreasing the chances of being able to fly at high altitudes for extended periods of time even more.

Can chickens fly naturally?

Why chickens fly in the wild.

In the wild, it's completely natural for them to fly. They use their wings to escape predators and to roost in trees at night. Staying on the ground would be far too dangerous.