This is only an issue when science credits are granted for such courses, while withholding from students the actual science which conflicts with such views. A small percentage of 'six day creationists' believe, for example. This in some cases leads to 'religiously correct' substitutions in courses dealing with geology, paleontology, astronomy, biology etc. Students taught this in the guise of science courses sometimes discredit themselves badly in the outside world. This doesn't happen in schools that teach theology separate from science, as most reputable schools do.
Skeptical activity focuses mainly on examining the truth of specific claims taught as science.
Most scientific skeptics have no quarrel with religion itself, which does not claim to be science. Most theologians agree that religious tenets can only be accepted on faith, and are not testable in the physical word. Articles refuting Noah's Flood, seven days of creation etc. I tire of these hacks of routine, who deny the dogma. I neither affirm nor deny.