I have the same issue, the more you play the career mode, and the more you progress the more you realize how broken it gets.
The VIP missions done with the Vision Jet always get me a negetive reputation dispite follwing the flight plan and every ATC instuction and a smooth landing, I still lose passenger satifaction, and respect airline procedure points.
I started VIP Charter mission with reputation S, now I am at C and going down the more missions I do without any fault of my own.