Without going into too much detail and making this a novel, the biggest difference is the Surface Pro has higher end hardware inside and runs a full copy of Windows 8. The Surface RT runs Windows RT, which is essentially a stripped down Windows 8, and can be compared more closely to Apple's iOS. The one bonus with the Surface RT though is that it does come with it's own 'RT' version of Office out of the box.
Okay, I was doing my own research the pro has usb 3.0, one is bigger than the other, and like the_prophecy said one is a PC and the other is not. So if I got the surface RT could I put Office 365 university edition on it?