I am not sure why there are so many negative ideas about academic affiliation. StartX is not the only startup accelerator around. Limiting themselves to founders with a Stanford affiliation differentiates them from others and allows them to heavily leverage existing networks. Disclaimer: I work at a StartX accelerated company.

As another commenter pointed out: Stanford is probably already investing in VC funds. This just lets them cut out the middle men, particularly considering they are required to invest along side other VCs.