A lot of the negative hype about soy is unsubstantiated hype. Apparently most of the studies that put it down have been contradicted by other studies - at least according to an article in Vegetarian Times. Natural soy products, that have not been highly processed, can be good in moderation.
Soy and thyroid - apparently it's an issue only if you actually have a real thyroid problem, and most people (even overweight) have healthy thyroids. If in doubt, a simple blood test can show if you are affected and should adjust your diet accordingly.
Basically you should avoid highly processed soy products and stick with more natural soy products like tofu. You should definitely avoid any Genetically Modified soy products which can be in just about everything. Read the labels and look for a statement that it is non-GMO. If it doesn't say non-GMO or organic, then it's genetically modified. So many products contain soy, even in small amounts, so it's very important to look for that statement.
Keep in mind that some of the healthiest and longest living people on the planet (Okinowa) eat soy daily (according to a 25yr study).
Just about anything can be bad for us if eaten in excess, and I think soy has been injected in our diets to the excess since it's a cheap ingredient that manufacturers promote as being healthy - so it ends up in everything.
According to
Food Revolution (John Robbins) It's true that soybeans contain substances that in excess can be harmful. But to imply, as some do, that as a result eating soyfoods poses a risk to human health is taking things much further than the evidence warrants. There would be dangers in eating a diet based entirely on soybeans. But, then, the same could be said for broccoli or any other healthy food. This is one of the reasons why varied diets are so important. Diversity protects. For most people under most circumstances, soy products are a healthful addition to a balanced diet that includes plenty of vegetables, whole grains, seeds, nuts, fruits, and other legumes. For most people, substituting soyfoods for some of the animal foods they now eat is one of the healthiest dietary changes they could make