The colors are in the textures.
If there are no textures, then the colors are in the model and you can't change them.
Well, you can, but you'll need MDLmat [freeware from Martin Wright Graphics] and you'll be very limited in what you can do.)
If the textures are in 256 color format you can work on them in any paint program, including MS Paint.
If they're in another format you'll need DXTbmp (freeware from Martin Wright Graphics) or ImageTool (freeware included in one of the MS FS9 SDKs, but I forget which one) to convert the textures to a format you can work on, then back into one that FS9 can see after you finish. (Note that FS9 can't "see" standard 24-bit bitmaps.)
It's easier than it sounds...
Beware - painting things can become addictive!