There's relatively easy technical measures you can take to suppress VoIP/Skype (in layman's terms, you block certain types of network traffic like voice over IP while allowing things like web pages). Some airlines with WiFi do this, in fact.

http://www.nytimes.com/2008/09/14/business/14essay.html

(Yes, you can defeat this. It's not the sort of thing that is trivial, though. You'd need some technical ability. And quite frankly, if someone is THAT desperate to Skype at 35,000 feet, let 'em and just have the flight attendants deal with them being loud and obnoxious.)

GoGo, the WiFi inflight carrier most USA carriers use, will be using Ka-band satellite within a few years (meaning the restriction on needing terrestrial antenna over land within range will go away soon):

http://www.gogoair.com/gogo/cms/technology.do

By all means, keep playing King Canute on the seashore and try to keep the digital tide from rushing into your airplanes, though...