I recall it being because Apple screwed up the licensing so bad ($1 per port) that everyone got together to create and then push USB 2.0 as a replacement even after the royalties got reduced to something semi-reasonable like 25c per device.
I worked at a place that developed FireWire peripherals. I can tell you the $1/port price never mattered to us, despite the loud backlash on the internet.
The real reason USB "won" is because Intel really pushed it and integrated it into every one of their chipsets. Possibly even licensing it to the other PC chipset makers for cheap/free up front.
Given that Intel is backing Thunderbolt, it stands a good chance at achieving the same widespread usage.
USB can easily be emulated and done using just the CPU, no chips required while Firewire required a real chip that did the negotiation and sat directly on the memory bus for DMA.
It sounds like Thunderbolt is "compatible" with USB and Firewire in the same way ExpressCard and CardBus are -- by putting the host controller that would normally be on a PCI/PCIe card on the bus.