There are many arguments for and against naive empiricism. Someone who subscribes to the philosophy may tell you that the goal of science is to uncover truth but that this cannot be accomplished when scientist's methods and interpretations are biased. Assumption causes scientists to arrive at some particular conclusion, which is justified by the experiment but still predetermined. Such conclusions cannot be said to be true becase assumption limits which possibilities are examined.
Naive Empiricism has been around for a very long time, and many arguments against the philosophy have developed. The rationale behind many of these arguments is that one must make some assumptions before any progress in study can be made. Assumptions don't have to be misleading or unfounded, but in order to study anything we must either make assumptions of some kind. If no such assumptions are made then science is limited to empirical observations which tell us little about how the world works. An entertaining work of fiction by a respected essayist, Jorge Luis Borges, Funes, the Memorious illustrates this position.
Also see: Epistemology