I'd say there're two problems: one is incentives, as you say; the other is making "apply these tools to your own beliefs" a natural affordance for people -- something that just springs to mind as a possibility, the way drinking a glass of liquid springs to mind on seeing it (even when you're not thirsty, or when the glass contains laundry detergent).

Regarding incentives: good question. If rationality does make peoples' lives better, but it makes their lives better in ways that aren't obvious in prospect, we may be able to "teach" incentives by making the potential benefits of rationality more obvious to the person's "near"-thinking system, so that the potential benefits can actually pull their behavior. (Humans are bad enough at getting to the gym, switching to more satisfying jobs in cases where this requires a bit of initial effort, etc., that peoples' lack of acted-on motivation to apply rationality to religion does not strongly imply a lack of inventives to do so.)

Regarding building a "try this on your own beliefs" affordance (so that The Bottom Line or other techniques just naturally spring to mind): Cognitive-Behavioral Therapy people explicitly teach the "now apply this method to your own beliefs, as they come up" steps, and then have people practice those steps as homework. We should do this with rationality as well (even in Eliezer's scenario where we skip mention of religion). The evidence for CBT's effectiveness is fairly good AFAICT; it's worth studying their teaching techniques.