I have the Sonnet USB PCI-e card in my 2008 Mac Pro.
It is this card:
http://www.amazon.com/Sonnet-USB2-E...1?ie=UTF8&s=electronics&qid=1279232344&sr=8-1
When plugged in to the card, my iPad charges. In fact, the iPad displays that it is charging. This is, of course, without any molex connection.
However, I noticed that the card emitted a high-pitched tone when charging the iPad. It wasn't loud, but it certainly was annoying. So, I simply switched some of my other USB connections to the new card, and plugged my iPad directly into one of the rear USB ports on the Mac Pro.
Perhaps your experience has been different because you have the 2006 model. I don't know.
I found another oddity with the Sonnet card. When my keyboard was connected to the card through the USB hub in my cinema display, I could not option-boot to a different drive. The computer would simply boot to the startup disk selected in system preferences; i.e., it would not show the available startup volumes when booting with the option key held down.