If the purchase by a non-profit its for their own final consumption, yes they pay the tax the same as any other consumer.Just to clairify, if a church bought a new roof or Bibles (not for resale), would they pay FairTax on them?
If the Bibles are given away and no charge is demanded for use of the church by the beneficiaries of its charitable services embodied in that property, there would be no tax.
OTOH, if someone associated with the church were to use that church as his own home, yes the materials going into that roof would be taxable in the same sense that a computer purchased by a business were to be used for purely personal consumption by the owners or employees of that business it would be taxable.