It is hardly a surprise that the cover of NCAA Football 11, out July 13, does not feature Tim Tebow with the Scriptures written on his eyeblack tape. That's not to say EA Sports has never allowed similar things before.
Reggie Bush, on the cover of NCAA 07 (click that picture to enlarge), gives a shout-out to San Diego with the 619 (its area code) written on his eyeblack. And it's hard to tell, but it looks like Larry Fitzgerald, who had the cover of NCAA Football 2005 has something written on his, obscured by the top bar of his facemask. The covers have long been known for gameday accuracy, including equipment and apparel-makers logos. So it's not like extraneous details get smudged or edited out.
So is this a double-standard in the case of Tebow, a deeply religious man who feels an obligation to express his faith? You betcha, but completely understandable. It's inappropriate and just plain bad business for EA Sports to make any endorsement of a religion, which is what this would be.
The inevitable sideshow spat over what is and isn't political, religious, offensive or, frankly, permissible led to the NCAA banning any such writing going forward. It's informally called the Tebow Rule because of his notoriety, and his use of "John 3:16" as the eyeblack message in the 2009 BCS National Title Game, which sent a surge of Google traffic looking up what verse it is. (Hint: It's probably the most important one to Christianity.)
Sure, this is religion, not politics (although for many, the two are immutable in this kind of context). But where do you draw the line on it, though? What if a Cal player won the Heisman in 2008 with a "No on 8" message on his eyeblack? (The slogan of those opposed to the California measure that overturned recognition of gay marriage.) I don't think he'd be on the cover of a video game with it, either, nor should he be.