Tofu is a goitregen, which means it can cause goiters, or large growths, on the thyroid and neck. It has been linked to causing cysts and both hyper and hypo thyroid issues. You can google Tofu and Thyroid and read up more on this. :)
In Japan they have issues with this, but not as much as you might think, because while tofu is a staple in their diet, they don't use it as a milk-substitute or protein-substitute like we do. When they eat it, it's usually in miso soup in very small amounts and accompanied by seaweed. The Iodine in the seaweed tends to balance out the effects of the tofu, unless of course they overdo the iodine, which is another thyroid killer at the wrong dosage. Lordy it can get complicated! :)