The problem is a component of the Western worldview that has been dominant since the Christian domination of Europe - the idea of anthropocentrism. Broadly defined, anthropocentrism is the idea that only humans and human institutions are deserving of ethical (moral consideration), and thereby, any value in the natural world, whether it be other species, ecosystems, etc., only has instrumental value. This means that under an anthropocentric worldview, things in nature only have value insofar as human ends are concerned - when human ends conflict with instrumental value, the value disappears. This is why you see things like "animals are all well and good, but we should still build here even if it will destroy the ecosystem." In this view, only humans and the direct products of human action have intrinsic value, or value in and of themselves.
What we need is a slight paradigm shift - we need to abandon anthropocentrism. In a holistic natural ethic, things in nature which don't accomplish human ends, such as members of other species, or intact ecosystems, have intrinsic value, and must be given ethical treatment even if that might conflict with human ends. For example, in a holistic ethic, we would not destroy a pristine pine forest just because the economic value of whatever we're building can feed ten starving children - and this goes in line with many of our moral intuitions. A thought experiment often used by environmental philosophers is the "last man" experiment. The idea is that there is only one human left alive - humans will inevitable go extinct. Would it be ethical for the man to destroy the balance of a functioning ecosystem to suit his ends, even though he is inevitably the last human?
How does this fit in with treatment of animals? Right now, we treat animals as largely having instrumental value - yes, treating them nicely is all well and good, but we have strip malls to build. We must stop treating animals as having instrumental value, and instead treat most them and ecosystems - even the entire biosphere - as having intrinsic value. This would not require some dystopian fantasy where modern society is dismantled, but it would change what we treat as being valuable. The enviroment, including the animals which live in it (which includes us by the way) must be treated as having moral value independent of human aspirations. That's not to say that "animals have more value" or "animals have less value" than humans - we cannot make ethical decisions by attempting some calculus of ethical value - that's the folly of utilitarian ethics. "Maximum good" is not a possible calculation to make, because values are qualitative, not quantitative - animals, ecosystems, humans, etc., all have different sorts of values and rights that interact in different ways depending on the circumstances.