I am quite familiar with those who believe in "indigo" children. It was introduced to me as a plausible reason for my son's Asperger's Syndrome and has been discussed at length on many AS sites.
The general lo-down is that it was created by one person who believes kids with ADD, ADHD and AS symptoms are "special beings" and then that person created the term "indigo", etc. It is not recognized by the medical professionals that I've talked with regarding AS. Personally, I think the whole thing was created to make a way to get the public to treat people in a more positive way. At least, I hope that's why this movement began.
Whatever it is, it is a goofy way of looking at people on the autism spectrum and those with ADD and ADHD. Goofy, hogwash, and nothing that is threatening, from what I've seen.