While a scientific theory can often be posed axiomatically, scientists do not consider the axioms to be ontologically true either. They are hypothetical assumptions whose usefulness can be measured in the correspondence of the theory's predictions with the outcomes of experiments. I fail to see the "faith" in this approach.
Additionally, it isn't necessary to make assumptions regarding the nature of an objective reality (or even whether or not such a thing exists). I need only note my observations and attempt to optimize a predictive model for future observations in order to carry out the algorithm of the scientific method. Ideas I may have about the ontological nature underlying my observations are, in fact, metaphysical. The scientific method does not address such things and it is perfectly possible to carry on the work of science without entertaining a particular assumption regarding the nature of reality. Science steadfastly concerns itself with things that can be perceived (with or without the help of instruments). Assumptions about the fundamental nature of things are not part of science. As Eric pointed out, they are not falsifiable. Those assumptions are, by definition, metaphysical.