I've heard that the issue is delivery. In the case of WQLN, Rogers insists that rebroadcasting the OTA digital signal is unacceptible. I've also heard that WQLN has been slow to adopt HD. Rogers can get a direct digital feed from WTVS, and wider distribution of that feeds defrays the cost among more viewers.
PBS is PBS. The amount of local content on these stations is shrinking as budget cuts hit home. If there's little differentiation between content, it's not hard to see why Rogers would prefer to deal with one program supplier instead of several.
Another "light at the end of the tunnel that turns out to be an onrushing locomotive" for public broadcasting is Internet distribution of programming as podcasts or streams. As high speed Internet becomes more widely available, and as the PBS/NPR audience continues to evolve digitally, local stations become less important IF they don't have any value-added content to add to the network programming.
Cable/satellite carriage rules need to make sure that local stations have equal access to the audience. Local stations need to make sure that THEIR websites are well-designed and user-friendly so that they become the NPR/PBS portal, not the national site.
The real danger is that budget cuts - like those in Pennsylvania - are turning local PBS/NPR outlets into little more than repeaters.