Because the human definition and understanding of morality is not one based in what is or is not natural. Morality concerns the suffering and happiness of others. If we based morals on simply what is or is not natural, then many of our ideas would be different.
For example, rape is very natural in the animal kingdom. Even amongst humans, rape was normal in many societies throughout history.
Killing other humans is natural. Even eating other humans is natural. We stopped doing that when we became 'civilised'- ie/ created social rules that excluded such activities.
Abortion, cloning, medication, synthetic limbs, contemporary forms of contraception, prolonging life in hospital by artificially means (tubes that control breathing etc.) are all unnatural.
What I am saying is, this world is one filled with suffering and pain. As selfish creatures who strive for survival, we are naturally capable and driven to cause such suffering to others for our own gain. Morality is something that has developed within us that makes us think twice about acting on our selfish whims. So we control ourselves.
So we try not to rape and kill and hurt others. In most cultures, people have been taught to look at animals as something inferior (Ie/ according to Christianity and in ancient Greek understandings, animals do not have souls and were created for man to feast upon. These histories and civilisations are the basis for our contemporary western cultures and have influenced our views on animals). We humans have done this in so many cases- for example, racism, sexism etc. And so we treat that other race or species with less care.
Looking at a human being or another animal with equality is a choice, and one that generally emerges through education. Most vegetarians choose to acknowledge that most animals experience pain and suffering as humans do, and so we extend our moral consideration to those animals as well.
What is natural is not necessarily what is moral. If that were not the case, then we'd feel nothing wrong about hunting and eating our fellow man.