It seems that the distinction has to do with evidence:
“F is a matter of faith” means “F is unsupported by evidence.”
If this is said of religious beliefs, however, it is clearly false.
For example, there is the evidence of testimony in favor of the claim that Jesus rose from the dead. One typically allows testimony to serve as evidence for a belief (for example, Jones believes that his friend Smith is at the store because Smith’s wife told him so, and she is not known to lie about such things).
Or, consider the arguments offered in favor of theism: the cosmological argument, teleological argument, ontological argument, moral argument, and more are given in support of religious belief. Thus, it would be false that there is no evidence for religious claims.
Sickler, B. (n.d.) Conflicts Between Science and Religion. Internet Encyclopaedia of Philosophy. Available http://iep.utm.edu/s-rel/. Last accessed 24th Jun 2013.