Magazine covers are the same as photos that appear in the paper. There is no payment at all. I'm sure there are special circumstances, like Tom Cruise's and Katie Holmes' baby. But athletes and celebrities sit down for cover shoots usually for the prestige of being on the cover or because they have something to promote.
As for commercials, I have no idea. But are "active" college athletes in those? I think they might appear in their college uniforms, but after their eligibility is up. Same thing with trading cards. Once their eligibility is up, they can do all of those things.