Ok, well I read the article linked now (my first response was directed more at the general idea of faith based funding) and there's one point that struck me in the article. If the government ASKED churches to make their facilities available, then it does make some amount of sense to reimburse them for that if the government is going to reimburse some of the costs.

I'm not saying it's a cut and dried issue, but it feels to wrong to say "hey, can we use your church to house some people? Ok? Great then. Yes we have this pile of money to help out with the costs of doing so, but we can't give any to you because your are religious."