As it is with all medical treatments available, you should always be critical and careful of how you interpret medical publications and reports.
First, be extremely careful with anecdotal reports and advertisement from companies that manufacture medications as well as non-pharmacologic devices (the classic example that comes to mind is magnet therapy).
It is human nature to try to extrapolate medical research results to the one condition that you may be suffering from. I submit that most of the reports on glucosamine chondroitin relate to arthritic aches and pains and not to the more common injuries that martial artists may suffer. In other words, although there may be some benefits to glucosamine in arthrits (and by the way I can tell you that there is not much convincing scientific data on this topic), most of our pains are related to sprains and strains with the uncommon and rare ligament tear that you could see, for example, in rotator cuff injuries. In here, glucosamine will probably not help much and you will be better off with anti-inflammatory drugs (always under the supervision and with the OK of your doctor) as well as non-pharmacologic treatments like thermal therapy or even full fledge physical therapy.
In my experience (I am a board-certified internist and cardiologist) glucosamine chondroitin does not usually help. I have discussed this with many orthopedic surgeons and sports medicine physicians, all of whom agree with me. I will say, however, that I have been told by many of my patients, that this chemical/drug works well for them.
Just be careful out there, and if you get injured in the dojo, always allow time to heal at your own pace; remember people heal at different speeds compared to othhers.