The short answer is yes.
You can use makeup, but it will rub/wash off much more quickly than on a non-silicone product because silicone is non-porous, and the pigment will not sink into the prosthetic in the same way. I've used rubber mask grease paint set with powder with some success, but it doesn't work that much better than "straight" makeup. I've also tried alcohol-based makeup (which is designed to stay on unless removed with 99% alcohol), and DIY PAX paints (which are a mixture of acrylic paint and prosaide, an FX prosthetics adhesive), neither of which were very good for this kind of project (the alcohol stuff rubbed off; maybe its properties only work on skin? And the PAX peeled and stuck to everything).
However, there are silicone-based paints that are used to color silicone. No other paints will "stick" permanently (and I'm not sure of how body safe they are). Only silicone sticks to silicone.
Silicone paints are very expensive (mostly because they only come in a multi-part system, each of which must be purchased separately). The Psycho Paint system from Smooth On is supposed to be very good, but you need to buy the base (
http://www.smooth-on.com/Silicone-Rubber-an/c2_1115_1198/index.html?catdepth=1) which will run you $23 for 8 ounces, and the pigments (
http://www.smooth-on.com/index.php?cPath=1128_1190) which will take another $30 for a small set of colors.
There is a less expensive option of using oil paints mixed with thinned-down silicone caulking which is sometimes used in FX settings. I believe Reel Magik uses this approach (I've been meaning to ask them to elaborate more on this; the quote that led me to believe that this is their approach was: "We use a special silicone tinted with custom colors that we create to color our silicone prosthetics. This silicone paint must be custom mixed each time,and is not something we could offer...it requires chemical thinners to bond the paint to the prosthic that can not be shipped").
At the moment, I'm trying to push myself to get started on trying the oil paint/caulking method on one of my Vixen dildos. I've just not felt up to DIYing, lately. But I will post a full review once I try it. In the mean time, I've promised to send along the instructions I've found to multiple folks on here. Maybe I can just create a separate post with them? I'm drawing upon two sources with similar approaches: one from the Our Doll forum and one from the amazing FX book, Special Effects Makeup for Stage and Screen by Todd Debreceni.