It seems that some consumers get utility from paying for the good. This isn't always true, and it does seem counter-intuitive at times. In fact, it often seems that consumers get utility from getting a "great deal," and we often hear them brag about their amazing feats of 80% off.
In this case, however, for a few different reasons, some consumers get utility for paying. It is the responsibility of the seller to try to maximize or enhance the utility for paying in order to increase revenue. They have a few tools to do this, including making a big deal about how some of their proceeds may go to charity and by thanking "viewers like you" who choose to pay more than $0 for the good in question, and whose contributions allow the producer to continue operating. They may also provide Internet Points in much the same way that that Stack Exchange and other sites do in order to help incentivize suppliers to provide quality content in exchange for zero dollars.
They can also be thought of as providing disutility, using some of the same tools, to those who don't pay.
And, as you mentioned, sellers often go with a PWYW scheme to improve market penetration, and this is often stressed. Sellers who need market penetration can typically pass as "indie," and flaunting their indieness may again improve the utility the consumers get by choosing to "support" them, the "little guy" or underdog. This brings to mind a couple of economic papers (which I can't seem to find at the moment) relating to horseracing and how it seems that people get utility from betting on the underdog to the point where it was once possible to have a positive expected value for betting on the favorite whenever the odds were above somewhere around 1:1 or 1:2.
Anyway, marketplaces for these goods tend to strongly emphasize this, doing whatever they can to promote their sellers as home-grown upstart startups, even putting it in their respective names, encouraging consumers who pay to think of themselves as supporters or patrons rather than consumers or even foolish rubes who paid for something that they could have gotten for the sum or $0.
To summarize, I think that those who choose to pay are actually purchasing the good in a bundle: the item being sold, along with some quantity of warm fuzzies. At a certain point, consumers either get no additional fuzzies or start getting anti-fuzzies (cold stabbies? Ice bricks?) for paying any more. Some consumers get no fuzzies for paying, or their willingness to pay for fuzzies is low, so they pay zero dollars. Sellers know this, so they are responsible for maximizing the quantity of fuzzies (perhaps by influencing consumers) and gaging how many consumers they can expect to get fuzzies before deciding to use PWYW. It's possible that the quality of the good being sold is related to the quantity of fuzzies that the buyer receives. That is to say, consumers may enjoy paying parties who make "good" goods, and they will likely feel ripped off if they voluntarily pay for a "lemon."