First, common sense should tell you that no newspaper is gonna give away content for free. THat said, you go into the app (just looked at the Boston Globe), scroll down, 'top in app purchases'...that means the app itself IS free. But the content is not.
Now do you have a point that maybe there should be more classifications in the app store, such as Free, Paid and Subscription, can't disagree. However, complaining at us accomplishes nothing. We're just users here and we have zero control over anything Apple and the other companies do.
What you can do is send them some feedback and tell Apple your concerns and thoughts. It'll go further than talking here.