$0.99 is nothing really, if you've already bought into the Apple ecosystem. It's just a nice way to drive people into the app store and make sure they have a credit card on file :)
Your title is confusing... Facetime for mac has just appeared, right? To say it's "now $0.99" doesn't make sense to me, unless I'm missing something.
But yes, why the hell are they charging for facetime at all?
My guess is it will be included with new Macs for free going forward, and only costs for existing Macs. Not sure, though, and doesn't seem to be a wise decision to charge for it in my opinion.