But you don't have to enter a contract with anyone to get that licensed software -- you can just buy it at retail. MPEG-LA would have to come after you somehow via the software's shrinkwrap EULAs (which have never been tested in court at all).
But the patents don't cover the process of making the files available to the public via HTTP supported by ads -- it would appear that these restrictions on that are a novelty of MPEG-LA's standard contracts for licensing the patents.
They're obviously enforceable on the organizations that entered into those licensing agreements directly, but what if I bought an licensed encoder off the shelf?
Is the on-disk format itself somehow patented, such that the files themselves are patented articles? Wouldn't that fail the machine-or-transformation test rather egregiously?
No no no, you're making the assuption that "buying an licensed encoder off the shelf" gives you some kind of patent license. It does not. It's a license to run the software from the manufacturer of the software. It sometimes contains a transferable license from the patent holders, for some purposes. Read carefully.
But walking into Fry's and buying a codec product off the shelf for $49.95 doesn't automatically allow you to start a video megasite.