Preserving earth (as in, not causing catastrophic environmental damage due to industrial expansion) is more expensive than keeping physical humans alive which is more expensive than only keeping humans alive as uploads.
Not saying this is likely, but if the AI is not speciesist in favor of humans (it does care about humans, but not more than e.g. whales or chimpanzees), then plans which end up protecting a large majority of humans look a whole lot more expensive overall.
Even if it does care more about human beings on an individual basis, I think the argument holds (unless the difference in caring is extremely large). Including them in the calculus at all would increase the cost a lot (just considering the sheer number of them, and the logistic challenges of untangling the complex interdependent web of natural ecosystems).