I don't think there's a general rule for this. It depends on local usage and personal preferences. As mentioned in the initial post, the choice may be geographical ("up" for north and "down" for south) but it could also have to do with the topography of the region. People will say "I'm going up the store" if it's uphill and "down to the bar" if it's downhill from where they are. If you live near the water, the waterfront is usually lower, so you will say "I'm going down to the waterfront".
But expressions like "up the road" and "down the road", or "come up" and "come down", are often interchangeable, especially when the terrain is flat.