Sometimes I have noticed the heat, but it is a intermittent thing. A USB port only puts out about 200 milliAmps anyway, not a whole lot of power. The wall charger for the iPhone puts out approximately 1 Amp.
Some of the ports on a computer do not have the full 200 mA because of other devices connected, as it appears you have found out. A hub will also have issues with power, unless it has it's own 5v power supply that plugs in the wall.
I have found USB devices to work rather poorly when there is more than one connector in between them, and the root hub on the computer. Except for maybe a memory stick or something small like that.
The iPhone definitely needs a full powered USB port.
Also, check your power management setup and be sure that the USB ports aren't going into a low power or off state to conserve power. If you are running a windows machine, go into the device manager, and under system devices (if I remember right, that is what it is called) near the bottom of the list, and expand the list. You should see some items that are listed as USB root hubs and such. On each root hub, double click on it to open the properties sheet and choose the power management tab. On this tab, uncheck the option that says "Turn this device off to save power", then apply. Do this for all of them and then close the device manager. This will manually stop all of your USB hubs from going into a sleep state while the computer is on.
Of course, if you have a Mac, just switch to a port that is not on a hub. Tower computers usually have USB ports on the back near the connectors for other various hardware. Those ports are directly connected to the motherboard and are part of the root hubs.
Sorry for the long post