There is no doubt as you said that the total number of animals suffering in what is usually referred as the natural world vastly exceeds the total number of suffering creatures directly exploited by the human race, however what we mean by the related statement is most of the suffering and not most of the sufferers.
The suffering in factory farms is much more intense. Take for example the billion battery caged chickens who are suffering every single moment during their two years of horrible imprisonment.
In addition, if you are familiar with our "vegan suffering" and "occupied territory" articles, where among other things we discuss some of the allegedly none direct suffering caused by humans which is actually absolutely direct as we argue in these articles and in many others as well, you can see that of course we take humans’ enormous pollution into account and also deforestation, global warming, desertification, habitat destruction, land destruction, land division, agriculture and etc.
Taking all of the above and many other factors into account, all in all we conclude that most of the suffering is caused by humans.
By the way usually we need to convince activists that they must do the best they can to stop the suffering caused to nonhuman animals by other nonhuman animals and believe it or not, that there is enough suffering in nature that can justify our solution, so it is a little bit strange (but positively refreshing) to address the natural suffering from the opposite direction of what we are used to.
For example someone asked how did we conclude that most of the creatures suffer most of the time assuming that except for predation, starvation and diseases creatures in nature are having good lives. We think you’ll find this discussion interesting. It is calle: "Most of the creatures suffer most of the time" and you can find it in this category.
In any case we don’t find this question relevant to the only one solution initiative. Either way we must find a way to stop all the suffering regardless of who is responsible for it.