It's a question of appealing to the best explanation. Intelligent design can explain the benefits of life and the utility of our organs and mental functions (they're designed by a benevolent deity). But this approach has trouble accounting for the downsides, the apparent evils and accidents that trouble us (which lead to the famous problem of evil for theistic religions).

By contrast, evolution by natural selection and naturalistic cosmology can explain the whole array of features we encounter, the good and the bad, by showing how order and disorder are bound to arise in any slow process riddled with mindless accidents.

Which worldview provides the best explanation of all the data? That's what's at issue here. The downside of evolution, and the problems with our body type count against the most optimistic religious analogies. It's fair to ask what kind of deity would create this kind of creature or this kind of universe, and it's fair to check whether that deity fits a certain religion's expectations.