I see that you can select a ship without cancelling its autopilot from the ship list, so why not just make that the default? That is, when you select a ship, the autopitlot just doesn't get cancelled. Maybe it stops, but if you don't change the destination, it will continue on eventually.
The ship list idea is nice--what I think eSnaffu might be getting at is something like a colored square around a ship's destination sector (or something finer-grained like a little circle) on the minimap when the ship is selected.
Here's an unrelated mini-map suggestion--when you select the "show stars", "show ships" etc. options, the items in question "flash" a few times on the minimap. If you like the idea, then maybe a sub-button for each category that triggers the flashing (or turns it on and off). If you want to go further, a way to pick a race and flash their assets (in the minimap!--get your mind out of the gutter! :D).
-Robert