I know too many smart highly-educated Christians to think that religion is merely some lack of applied thought. It's a choice they made, knowingly and subjectively, to have religious faith.
Skeptics seem to have this assumption that humans are inherently rational, and it's only those who are intellectually weak that let bad/illogical ideas into the mind. I'd argue that this is a bad model because we are forced throughout life to rely on incomplete/inaccurate information from a wide variety of sources... our senses, our emotions, our peers and society at large, etc. Our brains are a very muddy place that was never tidy and logically "clean" to begin with, but we make do (more or less). A purely skeptical species would go extinct questioning the need to plant crops, etc.,
The way I see it, rationality (and the engineered pursuit of it, science) is a skill that must be developed and subsequently imposed on various facets of our worldview. How we select those facets (and how vigorously we investigate them) is a strategic question ("what is my biggest blindspot?") that we're not well equipped to answer (they're called "blindspots" for a reason). And we ALL have blindspots of various topic and magnitude.
In the case of religion, it's particularly hard to investigate these blindspots because adherents have been strongly conditioned to self-identify with the cause. Their parents, friends, community, and everyone they trusted as a child told them "this is what we believe, it is the only way to live a good life, and everything outside of it is corrupt and destructive". Like Tevye says in Fiddler on the Roof, "tradition tells us who we are and what G-d expects of us".
Analytically re-evaluating one's faith as an adult requires a tremendous amount of courage and vigour. To do so, they must overcome:
- Religious instructions to defer to authority.
- Implied instructions to not question faith.
- Perceptions that questioning is risky and/or evil.
- The nastiness of some skeptics (e.g., living examples of the "evil" of questioning)
- Accusations that the questioner's "real problem" is something spiritual and not intellectual.
- Desperate feelings that the faith "has to be true", precluding need for further analysis.
- Anecdotal proofs and feel-good stories ("testimonies") that offer emotional evidence for faith.
- Single-shot ad hoc arguments (emotional or intellectual) that preclude comprehensive analysis
- Apologetics literature or speakers that sound convincing initially, esp. when presented without opposing views.
This is not the only way people leave their faith, but it's relevant to skeptics because it's the "rational" route. I suspect that those who use "emotional evidence" as their primary waypoints for evaluating complex situation have it easier... they see the history of Christanity's/Islam's treatment towards women or they consider how wholly abhorrent the concept of hell is, and then they proceed to reject the system that generated those ideas.
Instead of offering mockery (a tempting practice), skeptics would do better to (1) humbly remember that we all have blindspots, (2) that every population has smart and dumb individuals, (3) that believers make many valuable contributions to rationality/science, (4) and that social and emotional arguments against a faith can compliment their existing intellectual arguments.