I had read there were some issues with soy consumption - that the Japanese eat it moderately but it is balanced out by other foods they eat - ie iodine rich foods like kelp and seaweed.
Eg, potatoes (part of the deadly nightshade family) are linked with some types of arthritis - but they're only a problem for those sensitive to them. This doesn't mean they cause arthritis in the first place and doctors wouldn't advise everyone stop eating them just because of that link.
It works the same way with certain foods and IBS. Yep, some foods make you feel MUCH worse, but that doesn't mean they cause IBS and the general public should stop eating them.
Another problem with the health and diet industry is that people are too often looking for a miracle cure. If it were suddenly reported that liver was the most health giving food with all nutrients you could ever wish for and had anti-aging properties, would you suddenly add it by the kilo/pound (whatever way you measure!) to every meal and snack every day? (YUK!)
I suppose the answer is everything in moderation, like so many other things. I'm sure it's safer for adults to eat moderately than for babies. Mother nature intended babies to drink breast milk only - soy isn't intended for babies any more than cows milk - the proteins just aren't right.
Also, as soy products are supposed to contain oestrogenic substances, it makes sense to moderate your consumption. But you shouldn't really eat any one food to excess, should you, for a healthy BALANCED diet. I wouldn't take soy based supplements, but I do think adding soy to the average adult diet should be OK for most people.