I've heard of someone painting their Zodiac. But I can't remember for the life of me who. I wouldn't have a clue what they would use as far as paint. I almost think you'd be better off just giving it a good scrub with a Scotch Brite pad and taking a fine layer of the rubber off. I don't mean grinding it down. Just giving it a good cleaning.
I did a quick Google search and found this paint for Zodiac's. Here is a link to the website. The stuff is called Tuff Coat.
http://www.allinflatables.com/shopping/paint/index.html
Here is some contact information for them. Telephone: Toll free in Canada and USA: 1-888-309-0990 or call 1-604-533-0990 Fax: 1-604-533-0611
If the stuff works half as good as they say then it's worth a try.
Rob