Eye-black is not just used for Christian messages. Some players put their area codes on the eye black, which is gangsta for the neighborhood they control. I remember Reggie Bush had his L.A. area code on his when he played @ USC.
You are correct, and lots of gangbanger “playas” still do it. No doubt the NCAA would never have instituted this ban just for the bangers however, it took an eeeeevil Christian such as Tim Tebow to bring this important issue to a head. /sarc