A great deal of research funded by such organizations is done in combination with taxpayer funding, particularly with regard to infrastructure. As a cancer researcher I had funding from companies and foundations, but depended on my position in a tax-payer funded research lab to actually do the work.
According to the way stem cell research was segregated, those projects would have had to take place in buildings funded without taxes, staffed by researchers paid by private funds, using new equipment and materials, etc...