I honestly don't know how much of that article is hyperbole. It doesn't name any sources, either, which makes it hard for me to evaluate the validity of the points it makes.
It mentions animal tests--but come on, if you give rats enough of anything you'll start to see effects. How much soy do they have to feed the rats before effects start to show in their primary and secondary sex characteristics? How would that translate to a human diet?
I mean, saccharine was found to produce cancer in lab rats. A human would have to eat something like his body weight, per day, of saccharine, in order to match the saccharine intake of those rats which got cancer from it. So, how much soy do the rats eat, per day? How does that translate in terms of human diet?
I'm not saying the article is complete nonsense. Besides, we banned the use of Alar and cyclamates on the same kind of evidence as is presented in this article. The ban on DDT was not much better-supported than that, either. (To say nothing of the ban on CFCs. Don't get me started on that one.)
"Infertility"? Most infertility in the United States is caused by people waiting until their 40s to have children, specifically women. Younger women are more fertile than older women; that's a fact of nature.
Some of the "increase" in homosexuality is due entirely to society's changing attitudes towards it. Like ir or not, society is more permissive of such behavior these days; people are less apt to hide it. Estimates of how prevalent homosexuality is vary from 1% to 10%--I normally split the difference and say 5%, myself--and it's probably always been that way, at least since the fall of the Greek civilization.
(The Greeks, IIRC, practiced homosexuality as a form of birth control; but they also had marriage and the so-called "nuclear family", too. People had "bang buddies" but they also had spouses and children, and those disparate activities were not considered the same thing.)
Some of the "recent increase" is just people being less afraid of being ostracized for their homosexuality. You have to control for that; and I don't think that--given current data--there's any good way to do that. First everyone has to agree what is meant by "homosexual"; and while the answer to that seems obvious, it is only obvious when it's obvious. (For example, what about the otherwise straight man who enjoyes watching transsexual pornography? Is he gay? Some would argue that he is; others would argue that he isn't.)
Are there statistics showing any effect on girls? Do girls have larger breasts these days than formerly? Do they achieve menarche (begin to menstruate) sooner? Is puberty occurring earlier?
And if so, can we attribute this to soy products? Or is there some other factor in play?
In their story The Locusts, Larry Niven and Steven Barnes wonder what if sentience in humans is not a hard change to our genes?
When grasshoppers become too numerous, they change; they turn into a swarm which eats every plant in its path. In their story, Niven and Barnes observe what happens on a newly colonized planet when babies are born looking like neanderthals.
It turns out that the same is true on every other colony world, and even Earth itself--once the colonies were established, human babies started coming out neanderthal, rather than cro-magnon, with diminished intelligence and all. Human civilization had about eighty years left, give or take a decade; after that, it would all go away. The children had no use for civilization nor the intelligence to cope with it.
Humans, it was realized, were like grasshoppers--when we got too numerous, we changed, swarmed out into the universe...and then reverted to our pre-swarm state.
Some people say that the "rise" in homosexuality is due to this sort of effect, which is an appealing hypothesis even if there is absolutely zero evidence for it. It would make for a nicely self-contained population control device. Finding the "trigger" for this would take some doing; it's a non-trivial problem. And that assumes that this is even a valid hypothesis, which I doubt.
People seem very quick to blame modern society for ills both real and perceived. Frankly, I'm tired of people trying to get me all worried about the sky falling.