IMO, PBS has a lot more to gain, and to offer viewers, with the digital transition. From what I can tell, many if not most PBS affiliates are going to have a net gain in coverage and net gain in potential viewers after 2/17/09.
Furthermore, PBS offers more hours each day with HD programming than any other OTA station, and also offers more subchannels as well. Between the HD channels and the subchannels, furthermore, I would argue that there is more worthwhile, valuable programming compared to most commercial broadcasters. Commercial subchannels, with the exception of ion, tend to primarily consist of news and/or weather loops, or perhaps even a live feed of radar with NWS audio. On the other hand, PBS subchannels, varying by market, include Create, V-Me, PBS World, and locally programmed subchannels which may have 24 hour kids programming or are "statewide" channels like KET-KY or SCETV's SC Channel.
I also think that PBS stations tend to feel a greater responsibility toward OTA viewers. Perhaps this is because there must be some segment of the public that actively rejects commercial TV and therefore will "only watch PBS."
Something else to consider is that in some major markets like New York, Boston, Minneapolis-St.Paul, Los Angeles, etc. - PBS has at least two affiliates, giving them double the digital capacity of any other broadcaster in the market. Often, one station can carry a full quality HD signal, leaving the other one to carry a wide array of subchannels. Or, in other cases, each station may offer HD, and instead of squeezing in 3 or 4 subchannels with it, each station may only carry 1 or 2, but generally, they avoid duplication and this allows for a greater diversity of programming choices.