Were you using the version specifically for fabric?
The regular Aerospace 303 protectant is for rubber, plastic, leather, etc, not fabric.
I use that sh_t on everything ! (except fabric)
They sell a product specifically for convertible tops.
303® Fabric Convertible Top Kit
If you were using the fabric stuff, did you let it dry/cure completely before getting it wet? Also I believe you are supposed to apply it to a dry surface