It's pretty simple to make new "schemes" or skins. Go to "select aircraft". Pick a plane. Below that in the color scheme section click on "make new scheme" it will then save a "skin" of that particular plane for you as a .tga file. Go ahead and open it up in Photoshop and repaint it to your hearts desire. Save it as a .jpg file as it's a lot smaller and Real Flight still reads it just fine.

If you learn how to create new planes hang on as the requests are gonna pile in. I'm wondering why more hasn't been asked about making custom planes. At least I haven't seen much.