It's not saying taxpayers HAVE TO fund schools that also teach religion.  It's saying they can't EXCLUDE such schools just because they teach religion.  That would be religious discrimination.  

There's still the issue of whether to issue vouchers at all in any particular district, of course.  They have to decide that for themselves.  But IF you offer vouchers, and as long as a school meets all the academic and other requirements of other schools that qualify, then you can't DISQUALIFY a school just because they add a religious layer.  

Think of it like food stamps.  If the government is handing out food stamps to people based on economic need, it would be illegal for them to deny them to a person that meets the standard economic need but also happens to be religious.