Of course, we take things on faith. We take a leap of faith and believe that the people around us are not illusions or robots and that they are in fact made of the same sort of soul stuff that we are made of.
Life is full of leaps of faith. There is also the leap of faith that we have free will. Sam Harris has made it quite clear that under a rational, Newtonian paradigm, there is so room for free will. Our thoughts are determined by our biology, experiences, etc. Of course, it doesn't seem that way to us, and that seem is important. This is where the objectivity-obsessed atheists hit a bit of a bump; they are trying to arrive at 'objectivity' through their hopelessly subjective lens. They internalize existential leaps of faith, such as presuming they are not brains in vats, that life has meaning and shouldn't be destroyed etc,