I imagine most people who weren't very literate would also be stumped by things written fairly plainly.

From the way they describe how the message is read, it doesn't seem written very plainly at all. It would be odd to assume that this knowledge was accessible to many people if the manner in which it's written is only found in certain circumstances.

I believe enciphered hieroglyphics were covered by David Kahn in The Codebreakers. If memory serves, literate people wouldn't have too much difficulty solving them. The idea was the the plaintext would seem more significant to the reader/codebreaker after they labored for a few hours or a few days working it out. The labor required would add emphasis to what was being communicated.

I am looking at the last image in the article, captioned "The encrypted message instructs the viewer to appease the gods with offerings". The picture shows ... a person kneeling in front of a throned figure, offering something with both hands. Is something about this message supposed to be hidden?