In Chicago sits the Moody Church that has a subsidiary nonprofit with the mission: to seek to evangelize impoverished Chicago schoolchildren". While the nonprofit offers "after-school field trips, meals, tutoring and more for free" it also gives Bibles to every student, engages students in Bible study and religious activities, and requires that all staff members be Christian and measure its success by how many students become Christian." (See Chicago Tribune).
A Chicago Judge recently ruled that the religious nonprofit is exempt from paying unemployment taxes because, despite all the evidence to the contrary, the nonprofit is not a religious organization. It might be worth noting that the attorneys defending the nonprofit against the suit to pay unemployment taxes, were also the same folks that defended the anti-gay cake vendor.
That aside, the line that once separated church and state is growing thinner. Nonprofits get tax breaks because they are benefiting the public and NOT trying to convert them to one or another theology. Separation of church and state HAD once remained a significant part of the definition of what is the USA.
Ah, but so too were there many other definitions of what it meant to be the USA.