Is this the procedure you used?
Park your vehicle outside the garage.
Hold your original garage door remote one to three inches away from the in-vehicle HomeLink control buttons.
Simultaneously press the button on your remote control unit and the button you want to use on your in-vehicle HomeLink system.
Hold until the HomeLink indicator flashes repeatedly, then changes to solid.
Press the HomeLink button twice to activate.
If the HomeLink button operates the garage door, you’re done. If it doesn’t, and the HomeLink indicator flashes continuously, you have a “rolling code” system, and you will need to proceed to the next step:
In your garage, find the “smart” or “learn” button on your garage door opener motor (should be on the back near the hanging antenna wire).
Press and release the smart or learn button.
Within the next 30 seconds, return to your vehicle and press the desired HomeLink button three times.
If so, at what step did you have an issue?