No, they just run so many hospitals and as expenses increase while donations increase, that money dries up quickly. You would be shocked how much it costs to run a hospital, especially a hospital that provides services free, therefore all its operating expenses must be covered by donations. (BTW, it is my understanding that the Shriner’s hospitals also don't take government grants.)
For example, here are the financials from the Tampa Shriners Hospital.
http://www.guidestar.org/pqShowGsReport.do?npoId=262546&partner=justgive