The problem is that the entire map is on the lowest cliff level. Flying units over cliff level 0 behave as though they're over cliff level 1, which makes the ships fly 9 units above your 'ground'.
The trouble is that the game's x,y coordinate grid (for selecting and ordering units) is also based on cliff level 1. If you dropped the ships' flying height to say, -6, it would match the visibility radius more accurately, but then the ship would be flying around below the plane you issue orders on - which is also pretty horrible to look at and difficult to play.
Unclesatan's suggestion of height 0 is probably the best compromise between the two, but you might be able to get away with a -1. You would have to play with it and see what you like.
Edit: You might also try flattening the map out to cliff level 1, and using the Hide Terrain Cell brush to make the ground invisible.
Changed the Background and it is fixed, the problem was that the Background was way too low, so the light from ship had to Travel a lot. And since Background was way too far from the Train We couldn't find any way to fix it so we changed the background to a Dark Back ground and the Fog is hidden now