Well, it depends. If you click on the link in my other post above there are a number of pictures of stingray city with people interacting with them. You could also go to a web site like Webshots and search Stingray City and there are hundreds of photos. If your five year old can see the pictures of so many people (including kids) with the Rays maybe he won't be scared any more. The rays are harmless, I assure you, and quite friendly actually.
I'd still do the trip anyway because at worst case he wont go in at the sand bar but there are two other snorkel stops on the excursion with no stingrays and the grown ups shouldn't miss swimming with the rays. All snorkel boats have life jackets for the kids to wear so it is safe.
Let us know what you decide.