The basic reasoning in Apple's letter is pretty straightforward. Say you buy an iPhone. There's a boatload of technology in there that Apple has had to buy patents for, but you as a customer don't have to bother with that since any patent license Apple has obviously covers its customers as well. Apple is arguing that the same principle applies here; developers are merely customers of Apple's APIs and backends - and they don't need to care about any patents that cover these APIs and backends in the same way users don't have to care about the patents covering an iPhone.
"Thus, the technology that is targeted in your notice letters is technology that Apple is expressly licensed under the Lodsys patents to offer to Apple's App Makers. These licensed products and services enable Apple’s App Makers to communicate with end users through the use of Apple’s own licensed hardware, software, APIs, memory, servers, and interfaces, including Apple's App Store," Apple's letter reads, "Because Apple is licensed under Lodsys' patents to offer such technology to its App Makers, the App Makers are entitled to use this technology free from any infringement claims by Lodsys."
I'm no lawyers, of course, but Apple's reasoning here seems pretty sound to me. In the end, APIs are just part of an Apple product offering (say, an SDK), and developers are just users of that. They're not actually implementing any new code that itself infringes on Lodsys' patents, and as such.
Apple further states that the company will defend its application developers. "There is no basis for Lodsys' infringement allegations against Apple's App Makers. Apple intends to share this letter and the information set out herein with its App Makers and is fully prepared to defend Apple’s license rights," Sewell states.
Now we await Lodsys' response. I'm hoping Apple's letter is enough of a deterrent so that the small-time application developers don't have to worry.