It is an unskillful mental state, but we do it all the time. The meditator's job is to cancel this unskillful habit by examining it thoroughly, and then replacing it with another. Rather than noticing the differences between self and others, the meditator trains himself to notice similarities. He centers his attention on those factors that are universal to all life, things that will move him closer to others. Thus his comparison, if any, leads to feelings of kinship rather than feelings of estrangement.
Breathing is a universal process.
All vertebrates breathe in essentially the same manner. All living things exchange gasses with their environment in some way or other. This is one of the reasons that breathing is chosen as the focus of meditation. This does not mean that we shut our eyes to all the differences around us. It means simply that we de-emphasize contrasts and emphasize the universal factors.