I just hooked up the USB charger to an iPhone 3GS and 3G using two different cables and they both charged fine.
Some causes could be:
1. Positive and negative terminals installed incorrectly.
2. Bike battery is too low.
3. Faulty cable. (I've had many iphone/ipod cables fail. they would work when you jiggle them or bend the wire.)
4. Faulty USB charger? Try and charge a different device like an iPod or blackberry and see if it works.