Let it be, let it rust. Or clear coat it after it has changed to its amber color during oxidization. Have you ever noticed how landscape structures painted black get lost in the landscape? The natural amber tones of rust make a nice contrast with foliage and stands out much better.
I'm an artist who builds the canvasses for "your" bottle tree art. A bottle tree is an extension of you via the glass you decide to use. Your tree is an extension of your personality and therefore anything you put on your tree makes it especially unique.
My personal favorite are always antique bottles and glass insulators. They all vary in size, shape and color. Almost every major city has an annual antique bottle show and they're the greatest venue to buy bottles very inexpensively and to people watch. Check for one in your area and take the family for a bottle hunting expedition for the bottle tree. My other favorite source is my local glass recycling center. People throw away tons of bottles every day and you never know what you'll find.