I can see it being used as replacements for everything in the future. The Thunderbolt has 10GB throughput. USB 3.0 only has 5GB. Double the speed. Not to mention USB is monitored and run through software, (like the OS) and Firewire and Thunderbolt are run through it's hardware.
Theoretical throughput, not actual. Aside from Nikon and Apple, not many devices have a Thunderbolt port right now - and those that do most likely won't be supporting that limit.
Currently, USB 2.0 has it's speed up to 480Mbps, but how often do you see that in a device? I'm guessing hardly ever (if ever at all). It is not uncommon however to see firewire crank through more speeds.
Firewire took a good while after release to get up to its limit. By then, USB 3.0 will be more widely adopted and the manufacturers will be following the money to spend more time increasing USB 3.0's limit due to the wider adoption rate.
They go where the market is. It's been proven time and again.
The thunderbolt could easily be the system that could replace everything including DVI. Imagine a computer that only has 10 Thunderbolt ports in it.
Also, right now, a monitor requires around 9GBps. Even USB 3.0 cannot do that.
I can see monitors and high-end digital photography using it, but not for most portable hard drives, flash drives, peripherals, etc.
Those devices have to be able to connect to any computer and be operating system independent. Not only for functional purposes, but for business purposes as well.
Just as you want to be able to plug and go to share files with a friend, the manufacturer and retail stores don't want to have to stop production to make many different versions of the same product - it's costly to stop machines and change over, and even more costly to keep that amount of inventory.
Even with all that aside, the hardware right now just can't support that amount of throughput. Yeah 10gbps throughput sounds great on paper, and that's what Apple is after - more sales, but it's not not feasible. Even for the next couple years the hardware doesn't need it.
Right now, SATA 2 Hard drives (which just started shipping last year) runs a max of 3gbps. SATA 3 just started being worked on in late 2009 and won't be out for a couple years and runs at a max of 6gpbs throughput.
Since those are what are in most portable hard drives, there's no point in tying them to Thunderbolt when USB 3.0 will work just fine for the next 5 years.