I personally think that eating soy products that are as close to a whole soybean as possible are fine. It's the overly processed stuff that I'm concerned about. Tofu, soymilk, miso, tempeh, and edamame are all what I'd call "close to the source." Tofu dogs, soy burgers, and all the soy derived additives they add to food should probably be eaten rarely. If the ingredient list is long, I try to avoid it (I do that with most foods.)
You don't hear about the Japanese having excessive percentages of these diseases that they've linked to over consumption of soy. In fact, many diseases that are so prevalent in our society were almost non-existent in Japan until a westernized diet was introduced there.
It's like anything else, don't go crazy and only eat one thing. Over consumption of things widely considered good for you can be bad too. Also, since we are on the subject of protein, excessive meat consumption poses far more health risks then soy. If you eat a variety of foods you should be fine.
Here is a link that talks about how much is too much:
And a quote from that article:
"Recently, a few studies appeared showing potentially negative effects of consuming too much soy. One particularly troublesome study done in Hawaii suggested that men with higher tofu intake had more cognitive decline and brain atrophy with aging than men who ate little tofu.1 This data contradicts evidence that Japanese men, who consume tofu regularly, have better cognitive function and lower rates of Alzheimer's disease than American men.2 Obviously, more studies are needed to clarify these suggestive findings and to determine if there is something in tofu or related to tofu consumption that may be harmful. After reviewing these findings, Dr. Harris had soy products from Hawaii tested for aluminum levels and found a significantly higher level of aluminum in tofu from Hawaii than in tofu from the mainland. The aluminum factor may be a plausible explanation for the alleged "brain aging" properties of soy.
In any case, the evidence is not sufficient to warrant being fearful of consuming soybeans as part of a healthful diet. However, this brings to mind my basic theme of nutritional biodiversity--eat a variety of plant foods, and do not eat a soy-based diet."
I also wonder if some of these problems are due to the fact that a lot of the soy products we consume in the US are made from GMO soybeans. But they don't study the effects of that do they? I try to avoid GMO soy products, so I buy organic.