The breath is not a totally passive, automatic process. You are doing something to the breath, there is some level of the mind that’s making decisions.
"Exactly what are you doing with the breath right now? Is the breathing a totally passive, automatic process, or are you doing something to the breath? Is there some level of the mind that’s making decisions? One way to find out is to make conscious decisions about the breath, nudging it a little bit here, a little bit there. We’re not talking about making huge differences in the breath, just making gradual changes in whichever direction seems most comfortable." ~ Thanissaro Bhikkhu "Mastering Causality" (Meditations1)