I don't know too much about non-profit clinics as a whole in the country, but I do work at a non-profit faculty practice PT clinic in southern California. My boss (who's a PT and the director of my clinic) told me that there aren't as many non-profit clinics as there are for-profit clinics. Also, the pay is lower. The average PT salary at my clinic is 55k. It also seems pretty hard to get a job as a PT there since the majority of the PTs are graduates from the affiliated university. In addition to practicing at the clinic, they are also required to participate in scholarly activities at the university, e.g. teaching, research, etc. So it seems like a pretty tough job, as well.
So that's how it's like at my clinic. Hopefully others can give information on other non-profit clinics.