This rule was written with the intention of attempting to give both parties (the player on foot, and the enemy hog with or without a gunner) a fair chance at killing each other.
You're allowed to nade up elevated areas, because the enemy gunner would always still have a good chance of being able to shoot you as well. Even if the hog does not have a gunner, that player would still have a chance to attempt to run the player over. Either way, both parties are given a fair chance of being the victor.
You aren't allowed to nade down because it essentially is providing a distinct advantage towards the player on foot. In most (not all, Blood Gulch ledges, for example) situations, the player that is on the high ground could nade at the oncoming hog without the gunner having any chance to shoot that walker. Another situation is if a player is jumping down from a ledge, that person has a huge advantage over someone if they were allowed to nade before hitting the ground. To allow for both players to get an equal chance and let skill have a more dominant hand, it was felt that neither person should be allowed a distinct advantage like that.
Of course, there is one scenario that a player isn't allowed to nade up at. That situation is when you are in-between the Danger Canyon ramps in the middle of the map. Because of where that nav is located, you have to drive over the top of it, meaning your gunner would have no chance at all of shooting someone right in between the ramps.
Ultimately, it is simply to give a more level playing field to everyone, regardless of if you have to walk or if you're in a hog.
