Is your dog making any advances toward the cat? If he tries to sniff or follow the cat, the cat will be afraid. If the dog is just ignoring the cat, it will just take time for the cat to realize the dog isn't a threat.

Also, the cat may be telling the dog that he is in charge now, by hissing at the dog. If the cat is just running away, let him and don't let the dog follow.

My ex-stray cat, Mac, moved in about 6 months ago and promptly told all three dogs to back off! He wasn't too sure of the dogs, but now rules them all.