There are a few major issues with comics moving to the web. They share many of the same issues that comics in print do, but bear with me as I wander through this.
1) Availability - Now having been a small press publisher, I know the majors had an advantage on me because they could put out their comics faster and cheaper than i could. But, I still managed to keep up with my projected schedule and never missed a deadline with Diamond or my readers.
Small presses that are consistently late with delivering to the distributor are rather quickly dropped by the comic shops. They're tying too much money up in product that doesn't ever appear on their shelves.
Conversely . . . web comics seem to have a real issue with hitting deadlines. Probably because they're free, the creators don't seem to take it as seriously and honestly, it's tough to complain about the frequency of "free stuff". BUT, miss enough deadlines and it's easy to delink and move on.
If web comics want to replace print comics, the people on the web are going to have to take it seriously. I don't expect them to be like Bill Hollbrook, who's done Kevin and Kell as a web comic seven days a week since 1995 and hasn't missed a day (as well as doing two syndicated comics - On the Fastrack and Safe Havens). I do expect them though to set a reasonable schedule and meet it. If that means doing two comics a week, then do two comics a week. Build up a buffer and be ready to go incase you get sick. Don't be doing the comic the day you're supposed to post it.
2. Affordability - Currently most comics on the web are free. The creators make their money (if any) on donations and selling ancillary stuff. If they're lucky, they sell collections of the strips to people who want to be able to read a lot of strips without having to page through one by one. (Hmm, web comics make money selling print comics . . go figure).
If the big comic companies come to the web as their only means of distribution, then that's going to change the web comic paradigm. I don't see Marvel, Dark Horse or D.C. just posting several months of comics up and hoping someone will buy the trade paperback. Sure, it works for Phil and Kaja Foglio, but that's a two person team, not a major corporation. But after 15 years of getting free comics on line, will the viewers support pay for comics from the bigs? If not, what's the advantage to going web?
And I don't see that many "web comics" having the number of readers that rival any print comic and this is when they're free. I think their numbers would dry up if people had to pay for the web comic.
3. Piracy - The old bugaboo. Sure, people scan in comics now and share them on the web. But, if the comic companies want to make money on the web, there has to be a means for them to "make money". If people are going to take their web comics and release them into the wild (more than they do already), what's the benefit for the comic company?
You can only sell so many Wolverine t-shirts and PVC figures. If people aren't buying the comics (web or otherwise), then there's no more money for artists and writers. And believe me, there's little enough as is, unless you're really lucky or really good.
4. Presence - Print comics have enough trouble being found in the Diamond catalog unless you're with the big four. Web comics are damn near invisible unless you're lucky and stumble on a link from somewhere else. How do you find the ones you'd be interested in reading?
Web comics have the same problem that e-books have. You can't just go to a page, look at the cover art and read a quick synopsis of a web comic. You have to know it's there and then go to the web site and hope it's something you're interested in. I haven't found any "on-line comic store" that has web comics posted to browse the same way I can browse a comic shop and see what catches my eye.
So, to make a long story short (TOO LATE!), I can see comic companies having a presence on the web and doing stuff on the web, but until there's a way to successfully monitize their presence on the web, I don't see them abandoning print any time soon.