Eating meat is indeed natural in the sense that other animals do it as well. In fact, it is even done on occasion by our closest living relatives, the chimpanzees. However, there are many other things which are also natural. For example, chimpanzee males sometimes rape the females in their tribe. Chimpanzees sometimes engage in organized warfare against other tribes with which they compete for territory. A chimpanzee male, in a moment of rage, sometimes picks up a nearby infant, and crushes his skull against a rock. And chimpanzees do on occasion eat meat, and they do on occasion engage in cannibalism, in spite of the fact that there is a plentiful supply of food from other sources. So eating meat is indeed absolutely natural.
However, the fact that it is natural does not imply that it is ethically permissible. If we believed that eating meat was ethically permissible simply because other animals did it as well, then this would imply that there is nothing wrong with rape, cannibalism, or infanticide, all of which routinely occurs throughout the animal kingdom. The truth of the matter is that other animals share the darkest aspects of our humanity, as well as those aspects of which we are the most proud.