I think the issue with soy was that it increased estrogen production in large doses or something like that. I eat a lot of soy products, and haven't heard anything bad about it - of course, I wouldn't eat soy 3 times a day every day, or anything else for that matter.
The biggest thing that I've heard about soy milk is that people are substituting it for cow's milk, but it doesn't have calcium and vitamin D, so it's not a direct substitute in that respect. Just ensure that you are getting enough calcium!
I believe the SILK brand soy milk adds the calcium if that is a concern. Soy should be fine to eat since it has high amounts of protein. If you're wondering about eating things cooked with olestra, that may be a different story.
Are Soy Products O.K. During Pregnancy? 
