Kaepernick, along with tight end Vernon Davis, posed for ESPN magazine, a decision which Whitner believes will see them teased by the rest of the team.
"I would never do that," Whitner told CBS Sports. "To each his own. I don't know about all the naked pictures and the lower body. I'm a little bit against that, but to each his own.
"He's the man right now, and that's what he chose to do. But he's going to receive some flak in the locker room."
Kaepernick threw for 1,814 yards in his 13 games last season for the 49ers.