What is the message behind Twelve Monkeys Cover?

I took it to be an intentional misdirection since the 12 Monkeys are a MacGuffin, a

"...plot device in the form of some goal, desired object, or other motivator that the protagonist pursues, often with little or no narrative explanation. The specific nature of a MacGuffin is typically unimportant to the overall plot."

Plus, the placement in his eye brings extra focus to the idea that he's searching for them and that they are important and worth watching / pursuing. But, like any good MacGuffin, the search for the 12 Monkeys is a fruitless task. For good measure, the search also wastes "time" in multiple different times.

EDIT:

I'll add here that as MacGuffins go, The 12 Monkeys, and most, are usually trumped by The Maltese Falcon.

I also like @Coomie's ideas about the eyes.

Entire Answer is a Spoiler

IMHO:

In 12 Monkeys, James Cole (Bruce Willis) has seen the future. A dystopian future which is caused, in his mind, by the 12 monkeys. The symbol is over his eye because he has seen the damage that was caused. And his eyes are in shadow or sunken to represent the negativity of the future.

Note that the other characters are from the "present" and so have normal eyes.

I took the placement in Cole's eye (i.e. head) to symbolize the question of whether the whole thing is a delusion created by his mind, something he himself suspects later in the film.