Look at it this way...
If you look at the panel, and push the "-X" key that is pointing to the right, the table moves to the right. The table/part are moving in the cartesian coordinate system in a positive direction. The tool, IN RELATION TO THE PART, is moving in a negative direction.
There is no hidden agenda here. The TOOL moves negative when you press the "-" direction key. Obviously, the reverse is true when you push the "+" direction key.