NSLS-II, currently being built at BNL, has a total project cost of $912 million. LCLS, at SLAC, has a total project cost close to $350 million or so, but it's been estimated that they saved several hundred million reusing previous facilities from the linac (plus land) So, $1bn to build, plus operational costs which would be pricy. And you want one of each because a FEL is different than a synchrotron.
Now, for your $2bn+ops costs, you can service maybe 500 experiments a year, maybe a bit more, but less than the demand. At the labs, proposals for experiments that are generally picked are picked based off of merit, usefulness, promise, etc... not necessarily based on who can pay to use the facilities and what sort of profits could be tied to the research. You know... science, often done by tons of professors who get their money from the government as well.
Admittedly, the budget hits probably wouldn't affect the operations of these facilities too much, but they would definitely affect the people who propose to use these facilities. For example, the guys who did this research probably don't get their funding out of the operating costs of the SSRL.
So, yes, the government is the only entity that has invested this kind of money (largely through the DOE) to be able to do this on the scale that they do. I don't see any company picking up the slack anytime soon.
Lists of light sources: http://en.wikipedia.org/wiki/List_of_synchrotron_radiation_f...