Comments range from pathetic idiocy to scary, nasty, vile awful sociopathy. Moderating them would take a lot of people a lot time ($).
They generally serve no use.
One good use is for corrections. Articles are wrong a lot and it would be handy to have a place where those would go. Except, who would vet them, etc.?
Another reason is that most sites are giving up on having their own little social network thing. People are just moving to Facebook and such. Go to the Facebook page for the news site, flame all you want. It’s not the news site’s problem now, it’s Facebook’s. (I.e., no one’s.)