A double standard

Certain atheists reject the idea that they have to consider the best arguments for theism, thinking such arguments ought to be dismissed basically prima facie.  This type of response towards theism has come to be known as the Courtier’s Reply.  The force of the Courtier’s reply towards theism derives from an analogy with something supposedly just as ridiculous such as The Tooth Fairy or The Flying Spaghetti Monster.  The basic idea is this: the concept of theism is so ridiculous that one need not spend any time studying what others have said about such a concept in order to reject it.

So far, so good.

Concurrently, many of these same atheists will regale us with the triumphs and wonders of science, and the scientific method.  It helps us understand the natural world, helps us categorize, make certain predictions, and the like.  Indeed, it seems to me science is a nice thing, at least for those reasons.   But as the saying goes, too much of a good thing may do us harm.  Regarding the scientific method, when admiration turns into infatuation, sloppy thinking results.

Here’s the problem: the shorthand reason offered for holding the scientific method in such high esteem vis-a-vis theism (a false dichotomy in my book, but never mind) usually boils down to: “science works” (for example, see here, here, and here).  However, the justification for that position consists in actually implementing the scientific method: rigorous research, careful thought, refining and even overturning previous theories.  No self-respecting atheist-as-scientist would offer only the dismissive “science works” response when challenged to defend science against theism (again, notwithstanding the false choice here).  Further, no atheist-as-scientist would take seriously anyone who offered an out-of-hand rejection of a particular scientific theory without even understanding the relevant literature first.

But then, why is one justified in putting forth the Courtier’s Reply towards theism, but not the fruits of science?  What (non-question-begging) reasons could the atheist have for this?