What do Macs do differently so its USB ports can charge my iPad, but if I plug into a USB port on my PC I get the "not charging" message?
Because the iPad needs more than the 500 mA that the USB 2.0 spec says computers need to provide. Macwork has more information.
Apple's newer machines (and some newer PCs I believe) have got USB ports that are able to provide more current. The following Apple KB article explain better: