To be honest I'm not sure why Apple has allowed any of this in the past. Many app publishers are getting around Apple's cut for pay apps by charging subscription fees. Remember the Milk is charging $25/year to use their "free" iPhone app.
And there's the rub. RTM and others like are a separate service that also happen to have an iPhone app. Should Apple get a cut of your entire service now simply because you offer a free iPhone app? If I already have an SI subscription to the print magazine and they want to include a 'free' iPad subscription as part of the deal should Apple get a part of that?
I think no in both cases, but Apple seems to think yes. They have made themselves the only ones able to put apps on the iPhone and want to collect gatekeeper tolls. I don't like the sound of that and am hoping the ruling from Monday is only the first step towards setting up a legitimate alternative app store.