What is USB root hub?

Are your USB ports USB 2.0?

It is a common design for USB 2.0 ports to be managed by two controllers: one for low speed and full speed (the USB 1.1 speeds), and one for high speed (the new speed available beginning with USB 2.0). If this is the case, the 3rd root hub is probably from the EHCI controller managing the high speed connections, and the 1st and 2nd root hubs are probably from a pair of OHCI or UHCI controllers managing the low and full speed connections. Each USB port on your computer would then be connected to two of the controllers, the EHCI controller and one of the other two controllers, and which one is used would depend on the speed chosen by the USB device connected to that port.

You may have some internal ones if there is a PCI card. If you have a hub plugged in to expand the number of ports, that is there, too. And some device you have plugged in could have additional ports as well.

USBDView and USBView may help you sort out what is where.