Thunderbolt is not proprietary to Apple. It's an Intel + Apple thing, which I assume Intel will be marketing heavily and building into their motherboard reference designs. It shouldn't be too hard for Intel to get this into, for example, a Dell computer in the foreseable future.
Having said that, I would guess that it'll be at least a couple of years before many DACs are made with Thunderbolt instead of USB. 6moons reviewed the Wavelength Brick in 2005, and I'd guess it was around 2008 that we started to see an explosion of USB DACs out there, often with inferior USB implementations, and only in 2010 did we see a lot of better USB implementations. That's about 5 years between early adopter and larger product/market fit and acceptance.
Things have accelerated, so I'll peg it at 2 years minimum. And any manufacturer that chooses to go the Thunderbolt route will wonder if there are enough Thunderbolt equipped computers out there right now to make the investment worthwhile in the short term. Assuming that an average computer buyer replaces their computer no more frequently than once every 3 years, we're talking 3 years before there are sufficiently numerous computers out there with Thunderbolt.
Apogee is making the bet now because many of their pro customers are already on Macs, ready to adopt the latest Thunderbolt technology. I don't think we can say that's true for the broader audiophile community.