I like Henley's phrasing, "annoying but valuable," which sums up most independent comics fans' relationship with Fantagraphics. Their flagship news title, The Comics Journal, alternates between brilliant insight and arrogant diatribe. Or least it did; I haven't read it in years. For the most part I haven't read comics in years, period.
Back in the late '80s and early '90s, I read a handful of titles, mostly "funny animal" books--which back then Fantagraphics championed with multipage advertisements for their line. Since then, they not only dropped them all, they've come across as faintly disdainful of the whole genre, as if they're slightly embarrassed to have published Captain Jack, Usagi Yojimbo (still alive and well at Dark Horse) or the long-running anthology title Critters. Fantagraphics is one of the last of the Great Independent Publishers from my collecting days--Eclipse, Kitchen Sink, Mirage, and Comico are long gone, and Warp Graphics has reverted to All Elves All The Time. For nostalgia's sake--if only that, honestly--it'd be a shame to see them die.
Even so, I wonder if the problem for the field on the whole (not Fantagraphics, whose financial woes are only partially their own doing) is due to net comics. Not solely the cute but fluffy ones like User Friendly, but the damn-that's-impressive ones like Nowhere Girl, which is clearly the kind of stuff Fantagraphics would have been doing a few years ago. I'm pretty skeptical of the whole "the web will replace print" meme, but there are obvious upsides to lowering the barrier of entry in publishing.