Comparing a bad deal to a worse deal doesn't make it good.
I don't speak for the NYT but I've been following that chatter from news organizations for awhile. The thinking (right or wrong) goes like this:
* Publishers don't want to use Apples payment system as it locks them into Apple
* Publishers don't want to use iTunes for managing subscriptions
* Publishers don't want to have to pay 30% of the costs to pay for a service they don't want to use
There is a great and strong argument that its good for users and I agree with that. Users don't have to enter billing info etc across multiple apps. Thats a win, and a big one too.
However the reality is that when people grumble about paying for news content in the first place, and newspapers turn to the internet as publishing market shrinks, and the whole business model of news is in flux, along comes Apple and says we're going to take 30% for adding a service that you (the publisher) don't want and we're going to great a barrier between you and your customer so you're dependent on us.
This could be a huge debate, and I honestly can't go into one. Too tired. Too much to do today. So let me just say that you should always do what the consumer wants and in this case Apple is providing that.
But by a 30% cut they're going to make it difficult for news organizations to budget and pay for in-depth news coverage as they become increasingly dependent on online revenue sources.