2002 Honda Civic EX key fob issues?

I recently purchased a 2002 Honda Civic EX and I can't get an aftermarket key fob programmed. I replaced the head unit last week (I still have the factory stereo) and I'm wondering if that would have an effect on it? The power locks on the doors do work, but I'm wondering what could be the cause of the key fob issues.

My Mom had the same issue on her 2001 Civic EX. Unfortunately, you will probably have to bite the bullet and go to the dealer. I think it costed me about $180, which isn't awful compared to the price of replacing todays key fobs ($600+)!