When you open the contacts application, you'll see all of your contacts. However, if you open the phone application, and choose "Select contact", you'll only see those contacts you can call.

Right now, that also includes some of your IM contacts, due to bug 5732. With that fixed, by properly detecting the capabilities of your IM contacts, you should only see the contacts who can actually accept voice calls.

In addition, I've just filed bug 6835 about having the phone's contact viewer let you filter by the type of call you want to make.