I think the big problem with criticizing religious people for being irrational comes with the fact that most people aren’t scientists, and many, many people get through schooling without really getting an intuitive feel for when you should question a claim because the scientific method can’t deal with it.
Most people, even atheists and skeptics, have to take things on faith (more like probabilistic inference) at some point. You simply cannot be an expert in every field, you kind of just have to assume that the entirety of biological research isn’t based on a farce, or that those damned folks at CERN aren’t just making it up as they go along. This becomes easier when you work in scientific settings and have it verified to you constantly that the scientific method produces good results, which again, not many people have.
So then the breakdown for most people comes in "well, from where I’m standing, you’re asking me to trust those people over THERE (evolutionary biologists, physicists, archaeologists, linguists, etc) instead of the people I know and trust (pastor, parents, etc). If you don’t have a feel for what the scientific method is and why it works, the argument just comes down to “why should I trust the authority of a bunch of people I don’t know at a university using a method I’ve never seen work when it contradicts what all of these important figures in my life say?”
Even though it stems from a misunderstanding, I don’t think their conclusion is irrational from where they’re coming from. They, in their mind, have life experience with these people who have probably given them reason to trust them. They don’t, in their mind, really see why they should trust a bunch of strangers who haven’t really directly earned their trust. It’s really the same for a lot of skeptics, except we understand the value of the scientific method and the power of peer review so we don’t see why we should trust random conjecture or proven results.
Yes, I’d say from the outside skeptics, atheists etc have the more rational conclusion, but I can really see why a religious person might be hesitant to just cast aside what everybody around them is telling them in favor of a bunch of random people using the scientific method if they don’t really grasp why the scientific method (and peer review, etc) is so powerful.
ETA: Not to say that there aren’t scientists, even good ones, who believe in all manner of silly things. Those people are probably engaging in some double think or rationalization.