In YMAA, Dr. Yang's qigong theory states that the energy centers DO in fact have a "physical reality". We try to avoid getting too mystical, and instead research these ancient traditions with a modern scientific perspective.
These chakras, or energy centers, or matching cavity pairs, function as pumps or gates, regulating the flow of energy through our energy system.
According to most ancient traditions, these 7 energy centers exist within the body, and there are others which exist outside the body, on a higher dimensional plane, which cannot be seen, but can be experienced through training. Let's talk though about what we know and can easily research.
The lowest chakra, RED, relates to the Hui Yin cavity - the Yin meeting place in the body - the perenium, as well as that general area of the body from fron to back. It is called the Root chakra because the body connects through this gate to the Earth. The perenium and surrounding area is the physical location of this "chakra". The word chakra describes the function of this area of the body, which is, it acts as a pump for the energetic system, as well as a major energy gate in the body. The Indian sytem gets more involved in the emotions and levels of human evolution, both physical and spiritual, related to each energy center, but the correspondence, as Abersold said, is very clear.
The next one up, ORANGE, is the lower dan tian, and/or the correspondng gates on the belly and and back. The lower dan tian is physically located in the large and small intestines, and it is the main place where energy is stored and released in the body. It is considered to be the second brain, and is called the Enteric nervous system by western science.
Etc. Each chakra can be described from the Chinese tradition, and they do have a real, physical existence. They are not airy, fairy nonsense as so often they are described by people who do not know what they are talking about.
If you research each chakra, you'll see that the general experience of each corresponds between ancient Indian, Chinese, and other traditions, whatever these areas of the body are called.
Dr. Yang's books explain this system and these gates very clearly, without the nonsense you'll find from many other sources. I highly recommend you use them for your research.
For a more purely Indian view of these energy centers, this site is pretty detailed:
http://www.kheper.net/topics/chakras/chakras.htm