Painting over silicone caulk is, at best, a challenge. Because its surface, when dry, is slippery and repels moisture, chances are not good your paint will stick. But, if you simply don't like the color of your caulk and you feel you must paint, your best chance is to limit your paint to certain types. This will involve preparing the caulk surface.
Painting Silicone Caulk
Before painting caulk surfaces, use denatured alcohol to rub the surface. Also, try applying a thin coat of painter’s caulk, then applying your primer or finish paint. If you must paint, use a primer, then apply an oil-based paint. Latex is more likely to fail.