The key word here is multitasking, a major concept in modern operating systems. It is the ability of the operating system that allows it to run more than one application at the same time, something quite common with our computers, but not possible so far with mobile phones including the iPhone. Apple has built iPhone OS 4.0, the new operating system for the iPhone to be a multitasking OS, and VoIP applications are favored, because they will be allowed to run in the background.
Why VoIP is favored hasn't been explicitly stated, but the obvious reasons are the importance of VoIP as a key technology and hence money earner, and the fact that communication applications actually need to run alongside other applications because they achieve their purpose best when idle (rather than being off) ready to spring alive on any communication event, like a call.
So far, Skype on the iPhone was unable to receive calls - only outgoing calls were allowed. This is because Skype couldn't possibly run - and be the only one to do that - and be idle, waiting for an incoming call. Now that the OS allows applications to run simultaneously in the background, VoIP applications like Skype can sit idle, but on, in the background and pop up on an incoming call, just like with a PC. Furthermore, as cultofmac.com puts it, this will change the way iPhone users will view their quota or minutes - they can shift everything to unlimited VoIP on a flat rate. Now, wireless carriers have to follow, because AT&T's 3G on the iPhone with Skype is still a dark spot.