If he was seated on one end, I would put my child on the other end and put myself in between. If he was in the middle seat, I would offer him my end seat. Unless he was waving the magazine around or making it in any way so that she couldn't help but see beyond the cover, I would leave it at that.
His choice of reading material certainly wasn't very tasteful for a public place. However, given that he doesn't seem to know what is generally considered appropriate, I don't think it would be worthwhile to try and suggest an alternative magazine selection. The fact that he's reading what he's reading on a plane next to a child means that it's unlikely he'll understand a mom's point of view.
If the daughter brings it up later, it'd be a good opportunity to have a conversation on what she thinks of his behavior, how not everyone has the same concept of politeness or consideration of others, different ways of handling those types of situations, why we have smut, etc. She's at the age where she's becomming aware of stuff like that but may not understand it or have evaluated it very much. It'd be a perfect opportunity to help her figure out a little bit about this aspect of our culture and to help her think her way to a position on it. Of course, all this depends on the kid, depends on the parent, etc.
Reminds me of the stories you hear of Japanese men on subways reading the adult comics around the school children.