Have you ever been able to pair it with the car? If you have, and it's having issues.... you may need to delete it out of the system and start fresh. If you've never been able to get it to recognize, have you tried the walk through - http://automobiles.honda.com/handsfreelink/setup-your-phone.aspx
I had the galaxy s3 and it worked like a charm. For some reason my car won't even find the phone's Bluetooth to connect. I also tried with my moms iPhone 5 with no luck either. I don't think it's my phone
Michael all I could suggest is to make sure Bluetooth is turned on on your iPhone and try the instructions from scratch. Maybe delete your old phone from the car if it still shows in the system.
When I upgraded to the iPhone 5 from the 4s I think I had to delete my iPhone 4s if I'm not mistaken. If that doesn't work, maybe someone at the dealership can help.