Areas in blue indicate that they are just a broad area to find the pokemon. It can be in the grass or in a cave.
Areas in red indicate that you can't just encounter it. In the case of Heracross, it indicates that you can find it there if you slather honey on the tree. That's why Heracross' area is so widespread; Those are places with honey trees. It also can indicate that you need the super rod to catch it, or it's in a specialized area like the Safari Zone. There may be some other such circumstances that I can't recall.