school vouchers and the separation of church and state

I was surprised to find that some atheist activists get riled up over school vouchers. Hemant Mehta lays the issue out:

There’s one main reason church/state separation advocates don’t support school vouchers: It would allow parents to send their kids to religious schools on the taxpayer dime. (Want a second reason? The private schools also wouldn’t be held to the same accountability standards as the public schools.)
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Separation of church and state means that tax money cannot be used to fund one particular faith (or an “atheist school,” whatever that is) over another.

I think this is misguided. My libertarian instincts nudge me to view voucher programs favorably, because it seems to preserve the most choice for families, given mandatory, publicly funded education. Maybe I'm wrong on this, but I'd like to set that aside the policy merits for now. Do publicly funded school vouchers violate the separation of church and state?

I think the answer is no. Okay, under a school voucher regime, public money indeed finds itself going into the coffers of religious institutions operating schools. But the state is in no way respecting the establishment of any one religion over another, or over non-religion. In principle, the state is essentially doing nothing other than giving each student a backpack full of money and telling them to go get educated with it. It would be a different story if every student was given a voucher and only religious schools were on offer, but that isn't the case.

Imagine a church that decided to operate something like a health maintenance organization. And suppose, for the sake of argument, that the federal government decided to mandate the private purchase of health insurance but also subsidized that purchase. Would that also be violating the separation of church and state?

Is the Earned Income Tax Credit a violation of the Establishment Clause because some people are going to tithe or pay for vacation bible school with their tax rebates?

I suspect most atheists are opposed to school vouchers because most atheists are liberals and the school voucher idea is a darling of conservatives and libertarians. And that's fair enough. But the argument from church/state separation is weak at best, and it should not be a priority for atheist activists.