Honestly, just consider the minority of users who use ad blockers as loss leaders. Odds are, if the article is good enough, it may be shared and bring in other users that would not have normally come to the site and probably don't use an ad blocker.
Either way, there are enough news sources these days, if they want to actively encourage people not to use them as a source, somebody else will be welcoming.
How many stories have we seen where a virus was distributed by an online ad? No thank you. It is my job as a user to minimize the vectors that malware can creep into my system. Since ad networks have proven to be a vector, it is not only my prerogative, but perhaps my duty as a responsible user, to block them.