Excellent Article on Soy Toxicity in the SF Chron (linked)
I've been following the growing criticism of the modern, industrial soy industry for the past year, and this is some of the first "mainstream" publicity I've seen:
There are a lot of hippies in Berkeley freaking out today.
Personally, I am very suspicious of all highly processed foods. I'm not sure if the health concerns are really as bad as Dr. Daniel makes them out to be, but I don't believe that anything highly processed can be healthful. I do not eat soy burgers, TVP or other modern soy foods because they taste bad and they give me gas. And besides, humane and sustainable meat is better tasting, better for you and better for the environment (and, according to some proponents, better for the animals themselves) than "fake" meat.
Just goes to show you can make anything unhealthy.
Edit: however, people have known about toxicity in soy for ages. My mom won't make soy milk at home because traditionally it needs to be cooked several times to reduce toxicity and she says it's just too much trouble. My father remembers his mom cooking soy beans at least three times to make it safe for the family.