Glad you figured it out Aokie. I had the same problem when I started flying. For those that are reading this post and still don't understand how to hijack a ship you need to do the following:
1) disable the ship by targeting the engines. select the ] key on your keyboard until you see engines as a subcomponet target on the ship you are trying to disable. This technique will serve you well as you progress through your space missions.
2) once disabled, type /dock or you can select an icon for the same command if you have saved it to your toolbar at the top of the screen.
3) ship will dock and when you undock, ship will normally start up and begin moving. This is a good sign.