The best way to explain this, i hope, is to use an analogy.
Consider that the iphone or the ipod is like a water bottle that has run dry and needs to be refilled.
If you use a drinking straw size hose to fill it it will take much longer to fill than if you use a garden hose size hose to fill it. As long as the pressure out of the end of either hose is the same. The larger hose is capable of passing more water.
The voltage of the USB port is the same 5 volts if it is from the computer USB port or the dedicated USB power supply. It is like the pressure at the end of the hose.
The USB port on the computer can pass .5 amps of current.
The USB port on the dedicated power supply can pass 1 amp of current.
So the current is like the water and it is filling up the battery.
The dedicated power supply should take half as much time because it is passing twice as much current.
Some dedicated power supplies can pass 1.5 amps and higher.
My blackberry rapid charger is 1.8 amps and It rocks, I love it. Waaaayyy faster than plugging into a computer port.
So that explains why one is faster than the other but not why computer usb ports are low amperage.
It is because the USB ports on the computer are just soldered on to the circuit board in the computer. The circuit board has paper thin layers of copper to pass the current through. If the computer didn't limit the current through the thin copper it would overheat and burn up. It would be very fast, more like a pop and then the connection would be broken and never work again.
The dedicated power supplies use wire or thicker/wider circuit board traces that can take the higher amperage.
The other side of this is that the battery can only be charged so fast. It can't charge in seconds if you send it 100 amps. It has a maximum absorption of the current being sent to it.
As you experienced, the absorption of the iphone is higher than what the computer port can send to it.
So the iphone needn't know that is connected to a charger, it's just absorbing everything it is being sent and the charger can send more.
And if your motherboard had a special charger port, one that had more amperage it would absorb more and therefore charge faster.
Alot of those external USB hard drives have a USB cable that Y's out to two ends to plug into two USB ports on the computer and just the one end on the hard drive. Because the hard drive need more amperage than one USB port can supply. If you had that kind of cable for your iphone it should charge twice as fast.