Wow, anything to do with Apple and patents and some people freak out. As pointed out, this would need to be part of the GSM standard and thus be licensed on FRAND terms. Apple would end up maybe getting a fraction of a penny out of the GSM patent pool for handsets that use this. They aren't patenting it to be the only ones doing it, or to make money, they want to do it themselves because they think it can streamline the iPhone purchase process just a bit more.
It is also one less thing to go wrong. True, SIMs rarely go bad, but it can happen, and the slot on the phone can be physically damaged, etc. Plus Apple hates putting openings in the phone, and would love to someday have a completely sealed (and thereby waterproof) phone if they eliminated the SIM slot, used a magsafe or wireless charger, and made the dock connecter and earphone jack wireless.
In today's world you patent everything patentable you can for defensive purposes. Sometimes you might use those patents offensively to sue others into submission, or to try to make money, but every company takes out patents on things they come up with as a matter of course even if they are as non-evil as Google originally was.
Why would Apple want to use this to restrict the carriers you can use? There are supposedly over a million iPhones in use on T-mobiles network in the US, despite that carrier not being officially supported, and despite the fact that its 3G bands are different from what the iPhone supports so Edge is the fastest cellular data speed! Add in all the phones being used in China and elsewhere in the world and that's a lot of money Apple would stand to lose if they prevented you from using a different carrier. Apple has no incentive to prevent you from using PAYG SIMs when you travel, that's in your carrier's interest only. If Apple had the carrier's best interests at heart, there would be no Skype or other VOIP apps allowed and iOS 5.0 would not have added iMessage.