I have a Genie with rolling code as well. I had to push the button on the Garage Door Motor itself and then press the button within 30 seconds on the homlink. It does not work at all to hold your remote up to the homelink. At least in the number of tries that I did.

 

first you program the remote to the rearview mirror, then press the button on the motor followed by the button on the mirror again. With the rolling code openers, you need to do both steps, first to match the car with the remote, then learn the car to the motor. The directions in the link I posted above walk you through both steps.