No, probably not on account of it getting "Applefied". In its original design spec I could have seen it getting popular since it was basically just an external PCIe bus. Would have been easy to add on with a card, and could have been a candidate for replacing SATA internally. However, Apple threw a bunch of money at Intel to get them to change it and integrate it with DisplayPort. That serves Apple's goals of "cables BAD!" well in that you can now have less cables, but it means that it can't really be an addon for systems. Since it has to be integrated with DP, it has to integrate with both a display adapter and the PCIe bus, which means it has to be provided by the motherboard. There's no real way to add it on.
Well most boards aren't interested in spending the money to add it on since it is useless to most people. There aren't many thunderbolt devices and what there is tends to be pro-video stuff, which not many people use. So there is a decided lack of thunderbolt boards. Only Intel's highest end desktop board has it, and few people drop that kind of cash on a motherboard. Even for other things that have it, like HDDs, it makes little difference. USB3 is "just as fast" from a consumer perspective for HDDs. When you analyze system load and so on you see the advantage but a consumer doesn't, they just see that data transfer is fast and that's all that matters.
Add to that the fact that Apple's investment bought them a year of exclusivity, which is a sure fire way to lower interest in adoption from other companies, and well, here we are.
So I doubt it'll go anywhere, at least in its current incarnation.