What commercial role for university research facilities?

Over at Frogheart, nanotech blogger Maryse questions the dual role of university research facilities that also provide fee-for-service. These facilities, many of which are funded by the sort of infrastructure spending announced recently by the federal government, are expected to function as revenue streams in addition to supporting academic work of associated labs. As these become more common, how are the academic priorities and profit-generating activities going to live comfortably side by side?