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I tried the instructions in the manual and variations there-of. I almost gave up. One day I believe I tried just setting in the car, clearing it first, and then aiming the clicker at the homelink and pressing down both until it finally took. something like that, I should have written down what I did.
Are you sure you have Homelink? GM changed to a look a like product in 2006 that doesn't work very good. Homelink is a Johnson Controls product and the new ones are made by Lear.
When I programmed mine to turn on my water/methanol injection kit I followed the directions by pushing the remote and the Homelink button at the same time. However I found that my timing was slightly off and since the remote for the W/M kit only sends a signal once the Homelink was never getting the signal. The Homelink blinked as if it was learning though.
What I did was simply delay pushing the remote button, making sure that the Homelink button that you want to program is held down before you push the remote button. HTH
If your car is an 07, you have the Lear product, which does NOT function like a Homelink (which is far superior to Lear IMO.) I'm told that Lear has good support, but it's just not compatible with my openers.
Here is a link to add a Homelink (which is a far more flexible product than the Learcar that we have in our '07 vettes) to your vette. Now I have both a Learcar and Homelink in my 07 coupe and my 07 Z06.