The misgivings of many to the theory of evolution have been created by the very same scientific community that is now so concerned that its teaching is being squeezed out. In many cases, experimental evidence of the latter is used as evidence to insinuate the former. To some scientists the theory of evolution is an all-encompassing worldview in contradistinction to a theistic worldview. Such mixing of science, philosophy, and theology must be openly discussed. What people object to is the teaching of an atheistic worldview in the guise of science.
Scientists constantly make assumptions in order to build theories to explain and make predictions.
However, one must not use those very same assumptions and turn them around and claim them as facts. Clearly everything evolves. However, it is not self-evident to me that the fundamental question of origins is a truly scientific question. If not, then the answer must be sought in the very same places where we seek answers to questions regarding meaning, values, and purpose. One must never forget that an explanation of the totality of the human experience may lie outside the realm of science.