(Edit: I think I misread what you meant by 'flagging', since on HN that word means a user clicking a "flag" link to report that a submission is bad for HN.)
If you flag stories for that reason you'll eventually lose your flagging rights. HN's policy is: paywalls with workarounds are ok, users can supply workarounds in the threads, but complaints about paywalls and paywall policies are off topic.
The paywalls suck, of course, but banning NYT, WSJ, Economist, New Yorker, and all other such publications would suck worse. I realize not everyone agrees with this, but it seems the right call to me, which doesn't mean I like it any more than you do.
https://news.ycombinator.com/item?id=10178989
https://news.ycombinator.com/newsfaq.html
Lots more at https://hn.algolia.com/?sort=byDate&prefix=false&page=0&date... if anyone wants to read it.