Creator-ownership doesn't necessarily imply self-publishing. Robert Kirkman owns The Walking Dead but doesn't self-publish it. (Course, co-creator Tony Moore is none too happy about Kirkman's sole ownership -- creators can screw each other just as surely as publishers can screw creators.)
Course, where I assume you're going with this is that if you get a bad publishing deal, creator-ownership doesn't mean shit -- as in the case with Watchmen. Indeed, I recently linked a story where
Marvel attempted to claim ownership of a creator-owned book it published decades ago.
On the other hand, some people who sell their creations, or produce them as work-for-hire, DO wind up doing pretty well for themselves. Stan Lee and Bob Kane are both good examples -- and also examples of guys who pretty thoroughly fucked their co-creators. Conversely, Steve Bissette has wryly noted that the only collaborations he did with Alan Moore that he's able to profit from now are the work-for-hire ones, because Alan Moore has stonewalled reprints on any of their creator-owned books.
Self-publishing's got its own share of problems, of course, and the biggest is obscurity. While the Internet has made it easier to self-publish and therefore easier for someone to distribute a book (or any kind of work) without the need for a middleman, that also means there's that much more competition and that much less curation. For every Penny Arcade, PVP, Achewood, or Hark!, there are plenty of talented cartoonists languishing in obscurity (and even those four examples have turned to traditional publishers for their print collections).
TMNT's gotta be the biggest creator-owned success story in comics history, and even it turned into an acrimonious split between the two co-creators and eventually ended in the rights being sold to Viacom. On the other hand, both co-creators actually DO seem much happier now than they were twenty years ago.
And you know, as bad as things are today, they're not as bad as they used to be. Scott Kurtz is completely full of shit when he says all that stuff that happened to Kirby has been fixed now (look at the sad case of Robert L Washington III, co-creator of Static, who died last year and whose family had to turn to charity to get him a grave), but at least today there are royalties and equity deals. Chuck Dixon and Len Wein have made more money off Bane and Lucius Fox than Bill Finger ever did from Batman himself.
Ultimately what I'd like to see is a comic book industry that behaves more like the traditional book industry -- authors retain ownership, and are paid in a some combination of advances, page rates, and royalties.
I'm rambling. There's no easy fix. And this is legitimately devastating. We desperately need copyright reform, and I'd sure like for the SCOTUS to take a look at this and decide that no, the agreements the Siegel and Shuster heirs made in the 1990's did NOT waive their right to terminate the copyright transfer -- but with this Supreme Court I have a hard time seeing that happen.
Beyond that, though, is my unwavering belief that copyright should never have been extended past 56 years, and Superman should have been public domain by now.