Whether or not soy is bad for you depends on the individual. Here's my personal experience:
I became vegetarian a year ago, and oddly enough I started putting on weight like crazy (about 18 pounds, which for me, is a lot). I'm not an unhealthy vegetarian, who gorges on junk food! I attributed it to me hitting 30, and tried not to get too depressed about it. During all that time I had been drinking soy milk with my cereal every morning, and eating soy products probably 3 - 4 times a week.
For the past 6 months, I've tried dieting. Like, serious dieting, combined with exercise. Only about 1000 calories a day. I could NOT lose weight. Talk about depressing.
I started having some strange symptoms as time progressed...constantly cold hands and feet. Weird sleep patterns. Irritability. I went to the doctor and found out that I'm hypothyroid, which is not uncommon in women my age. I'm on medication for it.
I had high hopes that my thyroid meds would help me start losing weight, since inability to lose weight is a common symptom of hypothyroidism, but I had no luck there, despite continuing to diet and exercise. I continued to plug along with the diet and exercise, making no inroads.
Two weeks ago, I read some information about soy contributing to complications with hypothyroidism, and also causing weight gain in such situations. I dropped my soy intake immediately. I've lost 4 pounds already.
Could my soy intake have caused my hypothyroidism? Possibly. There's some claims about that in the media. On the other hand, hypothyroidism is common in women my age, so who knows? I DO believe that my soy intake combined with my hypothyroidism (whatever the initial cause of it) was causing my weight gain, and preventing me from losing weight. I'm now limiting my soy intake to no more than once a week, and am hoping to get down to my target weight within a few months.
My husband, on the other hand, eats soy almost every day, and has no issues. It all comes down to the individual -- everyone has certain things they can and can not eat.