That's a broad sort of answer with a broad (and unhelpful) answer. It's important to recognize that humans often rely on religion in order to square their senses of justice and empathy with a world that is unjust and callous. When someone is getting up in your grille about religion, it's because you aren't aligning with their understanding of the cosmos. And in general, atheists respond to this... "interest" with antagonism: "I refuse to humor your childish insistence on the sky god". It's been my experience that a polite willingness to humor the religion of others, as well as a projected confidence in one's own "spiritual journey", tends to blunt the attack. Consider: the Christian faithful often feel confident and comfortable assailing atheists in ways they would never come at a Jew or a Muslim. I have seen devout Episcopalians be happier that their kids have found Scientology than are still "lost" to atheism. If you can find some protective "spiritual" coloration you are likely to be camouflaged from their need for proselytization.
Its meant to be a broad answer. There isn't a concise way to explain the problem. I don't have it in me to type out a novel detailing the origins of the situation. Suffice to say that there is no amount of camouflage that will make someone decide to act loving instead of antagonistic towards their own child.
You're not wrong. But you're also giving too much credo to the problem being religion. It could easily be that "religion" is just an avatar for the concept of "adopt my ways completely and unquestionably" in which case it can be dumb shit like "date an African-American" or "listen to rap" or "vote democratic" and you're right- there's no room for dissent in that case. But you benefit from determining what the problem truly is. I spent several years at loggerheads with my in-laws over a panoply of symptoms that all boiled down to "we don't like having our ways challenged by outsiders" and after all, they'd already accommodated one new husband why should they be required to accommodate another. Problems still erupt but I'd be a moron to believe they're what they're ostensibly about.