Again, terrain is always going to be an issue. In cities you are not going to hover a ship without drawing the wrong type of attention. As I said, there is some sort of air traffic control in civilization. It is not like hovering a helicopter, but more like hovering a 747 or Herc in the middle of a city. Just not going to happen. As to rural settings, terrain is still an issue. Forests, mountains, crags, etc. will mean you can not get close to the ground. You may be able to find a clearing near by, but there will still be travel involved. Time to haul out the land speeder. I just don't see it as being an issue unless you make it one.
I'm not going for addressing an issue so much as I'm brainstorming an adventure idea based on an extended overland travel (wilderness, not urban) and I'm looking for ideas that would plausibly deny "we just fly the ship there" as a derailment.