Why did the Egyptians believe the gods controlled the workings of nature?

Answer 1

The ancient Egyptians thought that the gods both controlled and sustained the universe. They thought that the Goddess Maat controlled nature and directed the actions of the gods as well as the people.

Answer 2

The Egyptians were like many early religions. They started out viewing natural events (weather, animals, etc) as being blind, often violent forces. Then as they worked to understand those forces and how they could be manipulated to help people, they tended to become personified.

The Greeks have a great example of this: The titans were violent, destructive forces, typically oblivious to, if not entirely malevolent twoards, mankind. These were then defeated by the Gods who did nearly the same thing that the titans did, but they were easier for people to cope with because they were more human.