There are already a gajillion threads on this, but, to reiterate the points, there is some evidence that soy may not be as healthy as it is made out to be.
I am too lazy to get citations, but you can google around easily enough. Soy, in the form of tofu, has been correlated with increased risk of Alzheimer's in one study. In another, the phytoestrogens in soy were given a cautionary status with people who are susceptible to certain estrogen sensitive cancers. Some studies show that it may interfere with thyroid function as well.
Does that mean soy is dangerous? No. Typically the amounts used were quite high, and even then the evidence is not conclusive. Some people just cut it out all together, while others limit their consumption. I think limiting your consumption is a good plan for any food really. You aren't going to die if you have tofu once a year. I regularly eat tofu, although I am not consuming ten bricks of it a day.