I have a feeling that this question is kind of like asking, “Hey, is it just me, or do all those punk bands tend to be pretty critical of the government?” It seems to me that most of the webcomics I read make fun of religion, usually Christianity, quite a bit, and not in a “poking good natured fun, laughing with them” kind of way, but more of a “pointing and mocking, laughing at them”.
I would guess that this is due to comic artists tending to be young, hip, and above average in intelligence-- basically your typical college know-it-all atheist. Off the top of my head the comics I can think of that have had religion mocking comics are:
Russell’s Teapot
The Thinking Ape Blues
The Fart Party
Subnormality
Dresden Codak
Team Special Olympics
Saturday Morning Breakfast Cereal
Sin Fest
Mitch Clem’s various comics
And maybe XKCD, though I can’t think of any specific ones, the comic is overwhelmingly pro-science
Tom the Dancing Bug
Matt Bors
The exception, of course, would be probably the most popular of all webcomics, Penny Arcade. Gabe is a Christian, and Jesus is a recurring character who is portrayed in a favorable manner, though I think Tycho is maybe an atheist or at least not a Christian.
Are there any that I’m missing? Does this seem to be the trend in webcomics, or are there actually good religious webcomics out there?* I suppose it’s entirely possible that I like the comics that I do because the authors have the same sense of humor/personality traits as me.
*And yes, I know about Chick Tracts, but those are hilarious for reasons completely unintentional.