Why did the founding fathers protect freedom of the press in the Bill of Rights?

Because they knew that a government-controlled press could not properly serve its citizens, it would only tell the people what the government wanted them to hear. A good example being "Pravda" in the Soviet Union. The "free press" in the United States, while still not controlled by the govermnent, is mostly under the direction of large corporations which dictate the content of the newspapers, magazines, and TV networks they own, so except for small independent efforts it is no longer really free.