It's a Christian school. The objection is that they try to live by what they believe the Bible teaches. We don't see anyone on the left criticizing Islamic schools for believing and acting in accordance with their "rulebook."
There's one other factor in play here, too:
The left wants the union-controlled public schools to be the only option for most children. To do that, they have to make sure no competition can take root. Right now, there are three types of schools. The private non-sectarian academies are only available in the cities and suburbs—they'll be fine. The elites need those to keep their own children out of the public schools. The public schools are everywhere (I'll count the charter schools among these, since even though they're officially separate, they're still government subsidized). Then there are the Christian schools. Most places, even rural areas, have at least one Christian school.
So, they do everything within their power to discredit Christian education. That way, they have no option but to be forced into the public school system. Then the unions control the children, and so on...