Don't forget that you have lateral thrusters!
Your ship can move up and down and strafe left and right. Be sure to have these functions bound (By default on the keyboard they are bound to the Q and E keys for strafing and R and F keys for up and down)
Completely this, zero throttle once over the pad and then use thrusters to fine tune where your ship is until you're directly above the circle on the holo display of the pad. Then thrust down (once you've put your landing gear down).
The compass will also tell you where the pad is

Hollow means behind, solid means in front, I've slightly over shot the centre of the pad on this one but it's fine to thrust down onto the pad till you get the visual form the holo display. Or you can just point the nose of your ship directly at the centre of the pad and slow to a stop directly above it. then just lift your nose till it's facing the pad number end.