The EFF is requesting an exemption for "Computer programs that enable wireless telephone handsets to execute lawfully obtained software applications, where circumvention is accomplished for the sole purpose of enabling interoperability of such applications with computer programs on the telephone handset."
Apple's response indicates that they consider such an exemption inappropriate because it would violate their copyrights. As the EFF points out,"Running lawfully obtained software on a smart phone does not infringe copyright, nor does the process of jailbreaking a smart phone in order to accomplish this goal."
Apple's argument against this is that the iTunes App Store provides plenty of choice. The problem with this position is that it's ultimately Apple who gets to decide what's available,not developers or consumers. They reserve the right to turn down programs, or even remove them at any time.