No, it is the wood grain, it usally isn't the natural color but it is the natural grain, I have a flame maple top on my tele style guitar. The flame, stripe, quilt grain of maple is not found in every log, thats part of the reason it costs more, the other part is that it looks cool and everybody wants it. The finishes put on flame tops is usally tinted laquer or dye stains and clear laquer, the idea is to bring out the grain but not hide it. Also fancy woods are graded for clarity and figure, A, AA, AAA, and their are many different species that have unique figure but maple seems to be the most popular for guitars, maybe because it's one of the less expensive species, check out the price on some flamed Koa,... I hope that answers your questions, have you checked out some of the different wood options at
http://www.warmoth.com