Corporate badging aside, I think it clearly marks a danger zone at each end of the ground for the spectators and players alike (as Shane said). I really admire the simplicity of them - attention is heightened when the play is going on within them. They are a major marking on a ground for a game that (thankfully) has few markings and very few play interupting rules relating to them (such as offside calls). They also help the viewers spatially distinguish the particular dimensions of the oval.
Aussie rules football has only a few ground markings, and as such more things are possible - at times quite surprising and unexpected things. Having zones and other rules complicates the wonderful simplicity of the game. Certain things happen within the 50m areas and a whole variety of things occur between them. If you think about it and weigh up the other ground designations in other codes - hash marks, yard/metre lines, red/blue lines, endzones, etc - the lack of rules specifically to govern the play of the game based on the ground 'zones' keeps our game free flowing and restricts interpretive judgements from interrupting play.
The centre square, two goal squares and two 50m arcs is all there is - great, leave them alone and let the game go on.
