Why is losing readers who make you no money a bad thing?
It lowers their hosting costs therefore it actually makes them money. People who don't use adblock, whitelist, pay the fee for ad free all make wired money and will continue to read it.
Because ad tracking is all about reach. I use ad-blocking, but maybe 80% of my Facebook friends or Twitter followers don't. When I share an article, there are potentially 80% of my acquaintances who would see ads. If I never share it because I couldn't read it, there is zero potential.
Because there's more to success than simply the amount of people who click on your ads. They say 20% of their readers block ads, I would say that it's fair to assume that of those 20% maybe 5% would be willing to pay over $50 a year for reading their content or whitelist them, probably a smaller percentage of users will simply update their adblocking mechanism to keep browsing unbothered. Everyone else of those will simply stop visiting them. That's a possible 15% traffic drop.
It may not be traffic that gave them money directly like you pointed out but it's traffic from a fairly active crowd in social media, it's the people who link articles to them on places like our own HN, Twitter, /. or any number of other places. This effect leads to a drop in number of visitors who see ads which is a revenue drop.
I do like the subscription model (I'd like it better if it was a Freemium subscription model but alas it isn't), but I agree with the OP in believing that they'll backpedal this change before the end of the year.
It lowers their hosting costs therefore it actually makes them money. People who don't use adblock, whitelist, pay the fee for ad free all make wired money and will continue to read it.