As a result of a conversation I read online between my teacher and some other students, I decided to stop and really think about the bigger picture behind what it really means to be in alignment. Here's what I feel like I've learned so far.
First, it's about more than exercising to maintain a healthy weight, or to develop a specific muscle or area that you think would look better bigger. It's not really an "exercise" program at all, in the standard interpretation of the word (like t-tapp, or zumba, or tai bo). It's also about more than doing a particular move to reduce arterial plaque, or some other move so you can reduce your risk of a lower leg amputation.
Though I think it's things like the above mentioned (healthy weight, strong, keep all your limbs) which give the program it's initial appeal, it's nice to dig a bit deeper and realise that there's more to it. For me at this moment in time, it's about cultivating the connection and amplifying the communication between body and mind, and becoming aware that the two are more than linked...they are parts of the same entity. Feeling an emotion can contract a muscle, and cell death in the body can cause the feeling of anxiety.
It starts by getting your muscles at the right length, and then you start to really become in tune with your body. The communication becomes crystal clear just because you choose to pay attention (learning how to stand on one foot with your eyes closed is my favorite example of this). You realize that you have been in control of yourself since the start, and you begin to make better choices for your body. You realize that by choosing to use your body the way it was designed, you are both respecting yourself, and the incredible evolutionary design of the human machine.
After you apply all this stuff to your body, you realize you can apply it to your mind as well. You can stop repeating behaviors, and holding your mind in positions that are harmful. You learn to let go of thought patterns that aren't working like you consciously stop flexing a muscle that's pulling your skeleton out of alignment.
The concept can also be applied to your whole life in general. You choose to engage in behaviors and activities (including work) that benefit you and make you feel good. You refuse to sit on your tailbone because it's bad for your skeletal alignment, you refuse to work at a job you don't believe in because it's bad for your overall alignment.
In the process of learning to self evaluate, and self correct, to let go of habits and re-write motor programs, by learning to respect yourself by making better choices, you can live up to your human potential. To me, that's what it really means to be in alignment.