I think I might be for a similar reason such as how skeletons run from dogs: They are made of leaves. It's possible that creepers know that cats like to play with and attack loose, moving objects. Maybe it's that creeper's can suffer great damage from cats if they get ahold of them and break them apart. Cupa the creeper girl is afraid of them because she still has the memories of a creeper, even though she's in a human form, and doesn't know that in her form she cannot take much damage from a playful attack of a cat.

Actually the reason may be that in myth and many cultures, cats symbolize evil, or Satan (Thus why witches have black cats). This would mean they sybolize the Nether (a place where there are no creepers by the way). And no, I am not making this up, many believe things such as cats are witches that have changed their appearance, or that they are from Hell.

sssss cat meow creeper ahhhh!! me :3 i have a trap

mabey the eyptians knew how to kill creepers and sence eyptians worshiped cats creepers are now scard of them and scence ocoltes look a lot like cats creepers still run from them

best i can come up with