Even if they publish all of their stories online, you have to realize that newspapers typically have huge CapEx and/or fixed costs. If they want to keep a single print copy out there, there is a huge fixed cost to print the first paper copy. I know that there are ways to reduce the fixed cost, but that increases the marginal cost. Newspapers have optimized their businesses on the assumptions that they'll print lots of copies. The "crisis" in the industry is that they all realize that assumption won't be valid sometime between now and "real soon now".
The internet is quite simply a MORE EFFICIENT way to sells news. It costs less to produce, distribute, and sell. So much less, in fact, that for existing businesses (newspaper co's) it's very difficult to make the transition without the entire thing collapsing.
The smaller newspapers are having more success at this than the big ones because their investments are lower than the big guys. They also are in a different news business; they do LOCAL news. Thus, they have unique content with less competition. All of the big newspapers are essentially the same national news, and that is very competitive due to the internet.
It's also not just a matter of "moving content online". Newspapers get ~75% of revenue from ads (display ads + classifieds, about half & half), ~18% from subscriptions, and a few other sources. The classifieds business kinda got stolen out from under their noses (see craigslist) and that killed about 25% of their revenue. Online ads are more trackable, and work better, so that reduced the VALUE of the same print ads. And subscriptions are down. Take nearly any business and tell them their revenues will drop by at least half and stay that way and see how well they do...