When scientific thought and mathematical logic became ways to perceive the world and demonstrate its principles reliably, I think some of those in power, who wanted to preserve increase their power and prosperity, but who also based that power and prosperity on deceiving or exploiting others, saw a danger in too much good thinking, sound reason, and organized, publicly-available learning. It would quite simply produce a population that could ask very good questions in very large numbers, questions that would make those powerful and prosperous uncomfortable. Also handy to them were certain religious tenets – the Bible is one example of a book of faith that is full of them – that asserted that faith is more important than knowledge. They used and promoted this – sometimes by paying and popularizing willing preachers – to sway the faith culture to put less value in families making their children smart, or communities encouraging tough questions and active intellectually-sound discussions as part of society’s best practices and discourse.
So the “war on Christianity” of which you speak is, for me, the war – and I don’t think we’re winning it – on those forces that misuse and corrupt Christianity to be a big tool to encourage ignorance and manipulate all the gullible minds thus encouraged to remain so. That science has exposed more and more religious thought to be simply untrue on a literal level (albeit perhaps still quite true and valuable on other levels) does in fact make it at least partially equal to a war on ignorance. As shown by the Rise of Trump and its consequences, ignorance is literally killing us. And if it comes wrapped in faith, it’s no better than if it comes wrapped in patriotism.