I think its more like if Google had also developed their own standard for sending pages to replace HTML/JS/CSS, replaced DNS with their own page discovery system, provided tons of pre-built reusable components that make up almost all parts of most sites, and then paid for all of the bandwidth for transferring webapps using this new system.
And then, still supported the old way of doing things, only charging a cut if you used their new system.
Apple doesn't charge me (or Valve) anything to buy something from Steam for Mac.
Likewise, they don't charge me when Netflix streams a movie on my Macbook.
It's their _market_ that they impose fees on. Amazon charges their Marketplace sellers up to 25% "referral fee" for all sales. Kindle market is 30% as well, I believe. Valve also takes a cut on both "retail" versions and DLC packs released through Steam. There were companies (like Introversion, who makes the awesome Darwinia and Multiwinia RTS games) that almost went bankrupt if it wasn't for Steams mighty distribution service and marketing (dare I say) genius.
What I don't get is, if NYT and other publishers are so ginned up about Apple's cut, why don't they just say "Hey, iPad users, go to NYTimes.com and subscribe. You'll receive the same hard-hitting journalism and insightful commentary in the Safari-optimized nytimes.com edition as you would from our iPad App. Subscribe today!" Problem solved.
wrt "why dont they just say": Apple prohibits "links" off-app subscription sites. It likely they'll take a dim of plain text too (obviously clickable links are not allowed).
I can kinda sorta understand Amazon charging the Marketplace guys (although 25% seems excessive), since they're targeting the long tail who would otherwise be invisible.
Obviously, I think Amazon charging publishers 30% to reach Kindle owners is bullshit, just as I think about Apple.
And then, still supported the old way of doing things, only charging a cut if you used their new system.