Yuval Levin sheds some light on why the NIH decided not to fund research on cloned embryos:

In a phone conference with reporters after today's announcement, the director of the NIH was asked several times to explain why the agency excluded cloning and the creation of embryos for research and his answer each time was that at this point to his knowledge there are no lines produced from those sources and that the NIH can review these rules as the scientific times change, since they are agency rules and not an executive order or statute. The language of the rules and of the director in that call suggests this is a tactical decision not to get ahead of the scientists (and pay a needless political cost), so as to be able to keep up with them in the future. Not encouraging, but again it could be worse. It could be worse above all because these rules have a practical and a symbolic significance. In practical terms, the NIH will now be able to fund just about all ongoing embryonic stem cell research with taxpayer dollars. But in symbolic terms, the message this sends is that even the NIH, even when left to itself and unconstrained by political masters, has to acknowledge that the destruction of embryos for research is not an innocent and unproblematic practice, but must be constrained for ethical reasons.