A few fitness professionals I know have been railing against soy for a while now, denouncing it as a poison that should be removed from all diets. They gave, as references, this website: http://www.endalldisease.com/?p=57 and mention the Weston A. Price foundation over and over.
This argument gives further reason to make sure you know where your research is coming from, and what, exactly, it is saying.
Let's take the studies that are referenced in this website. One says that soy in moderation (as in Asian diets) reduces breast cancer; it's just when it's in excess that you might see problems. One says that it helps prevent colorectal cancer in women, and has no effect in men. And one says that in mice (not humans), there might be a very slight decrease in fertility when a lot of soy is consumed. I'm having trouble seeing the poison.
Meanwhile, the Weston A. Price Foundation, while commendable for their work in promoting a non-processed foods diet, really loves to promote a diet heavy in meat and raw milk. They claim not to have interests in the dairy or meat industry, but a large percentage of their members (read: sponsors) are farmers. In addition, they held a conference in 2009 which was sponsored by Green Pasture, Vital Choice, and U.S. Wellness Meats-- all meat and dairy product companies. So this makes me question their bias.
I do a lot of research on the subject of nutrition, and I have seen very little in the way of valid studies that say moderate soy intake is detrimental-- quite the opposite, actually. There are countless studies showing soy's beneficial effects on hot flashes, certain cancers, and heart disease, particularly when meat intake is reduced or eliminated.
That having been said, PROCESSED soy is generally not a good idea (and, of course, neither are most processed foods), and soy in very large amounts is also not a good idea (as is the case with just about any food other than green vegetables). Soy should not be consumed by people who have thyroid issues or by infants. Soy is a common allergen, so obviously, if you have an allergy to soy, you should not be eating it. However, for a normal, healthy adult population, soy IN MODERATION can absolutely be part of a healthy diet. I'd take it one step further and say that, as a general rule, stick with sprouted and fermented soy. They are the most nutritionally dense and easiest to digest forms of the product.