Because they're taking issue with the things like magic, subservience to a church, historical scriptural fraud, conflict with science, and most importantly the religious condemnation of "vice" in general: they want their funtime treats like drugs and free access to women's bodies, and they think theocrats are ruining their good time in the name of something silly, irrational, and cringe. They don't have a principled opposition to the cruelty and bigotry of theocrats, because they come from the same chauvinist cultural background and have much the same material interests as their fundamentalist counterparts. You generally need an actual ethical framework and political education to shake free of the chauvinist brainworms American society tries to infect everyone with.

Like if you look at countercultural media depictions of evangelicals, it's usually like "oh they're too goody goody, they're too pure, they don't know how to have fun, they're silly and cringe, and the worst they can do is get in the way of my good time!" instead of "they are ontologically evil demons of hatred disguised in human skin and enacting horrors upon the world," and that's because the take is radically different depending on who's making it. Like a comfortable white cishet male atheist is going to have wildly different conflicts with evangelical theocracy than a queer woman is, and the former is platformed way more and has way more cultural power than the latter.

And that's why so many of the New Atheists went on to become secular fascists or tradcath fascists, because those promised them their funtime treats and they realized that the cynical hypocrisy of the system was a feature in their favor and not a glitch.