The idea that chakras are actual physical "things" is extremely doubtful (kundalini is a real thing though - and don't argue with me :), but as a model for psychological processes and insights, the chakra system is superior to anything Freud concocted.
I'd recommend Anodea Judith's "Eastern Body, Western Mind" for a solid introduction - she has a master's in clinical psych and it's a good book that isn't all new age BS, though you do have to be willing to try and understand how metaphors work... it's just a model, much like software is really only insubstantial thought-stuff that through the interface of hardware, actually can interact with the world.
The problem with a lot of "New Agers" is that they can't think abstractly - they are like the early Christians who got laughed at by the pagans for believing their version of the "dead and resurrected god" myth was the literal truth. But from a psychological angle, such a myth is very informative about something part of the "human condition".
If you think of "chakra talk" as a particular dialect some people use to communicate where their emotional and mental state is at, you can hear the truth of what they are trying to say.
It's pretty hard to describe something so outside the everyday experience with 'normal' words - I try to view such 'mumbo jumbo' as just another metaphor, doesn't have to mean something supernatural is going in.
There has actually been research performed recently, touched on here[1] which tells us that the body does actually communicate with the brain quite a bit-- it's not so much pre-science any more.
That has little to do with chacras, alignment and other such stuff though -- the same way that the fact that we have an electrical field around our body doesn't validate Kirlian photography of "auras".
You know that that is mumbo jumbo BS, right?