Here's what worked for me, simply follow these steps.
Open the C&C:Online launcher and use the Hook menu to hook your game.
I. Go into Steam and create a desktop shortcut for your game.
II. Open the C&C:Online launcher and go to the hooking menu. Hook your game. When Hooking, you should receive a prompt asking for your confirmation, this is how you know it worked. If you don't receive anything and you are still not able to launch your game, check your anti-virus (Norton especially) as they are known to delete the hooking file. Add an exception for C&C:Online. Make sure that you Hook the game after you have made the Steam short cut and not before.
III. Launch the game using the shortcut Steam made for it on your desktop. The launcher should pop up, so select your game and off you go