So let me get this straight, USB 3.1 is much much cheaper, uses simple cables with no electronics inside, is fully backward compatible and is ubiquitous while Thunderbolt is expensive, exclusively high-end, rare and requires cables with fancy chips inside, without actually being faster?
Sure, Thunderbolt 2 will be even faster, but then so will USB 3.2 and so on...
the problem with your logic breaks down like this...
thunderbolt 1.0 = exists in reality.
usb 3.1 = theoretical, and only exists in a lab.
thunderbolt 2.0 would be on the same phantom existence scale as usb 3.1 for now, but we are pretty much guaranteed its arrival in the next coming months.
as far as your other points, you obviously have no experience with fibre channel, 10gb ethernet, etc. all of which have fancy connectors along with "chips inside". an active twinax cable is about on par with a thunderbolt cable for comparability. other technologies have the same paradigm for high bandwidth connectivity. apple creating a cable with chips in it is not new, and they didn't do it to piss people off. they wouldn't be in business if that was their goal.
as others have mentioned, it's all about use case. i mean why are you not bagging on dvi and how much better hdmi is? now that 4k is becoming readily available for consumers, 1080p must be garbage too. bottom line, someone has to come up with a technology first. i think the crux to everyone's beef with thunderbolt is the exclusivity apple is putting on it. if it was available on mainstream "pc" systems, everyone would be using it. firewire was a perfect example, where usb 1.x did not cut the mustard for connectivity for certain devices, mainly for high i/o storage & streaming. so "firewire" as we all know and love it now, was born. then usb 2.0 came out (which still is trumped by fw400), then the next evolution of firewire (fw800) was developed and so on. at what point in time do we all wait around for one single organization to develop or improve on technology? some people aren't content with the current environment and opt to inject their own ideas to improve things. cisco is a great example of this. they are another "evil tech giant" that gets a lot of guff for expensive & proprietary technology. but what people fail to realize in that industry, is that big bad giant created the majority of the "standard" technologies (mpls, trunking, etc) for the sake that they just didn't exist, and then allowed others to adapt "open" or standards versions of the same technology. the way i see it, apple saw a lull and got on board with intel to help bring light peak / thunderbolt to market. i think at this point, that thunderbolt has leap frogged the industry and we ended up with a cool technology no one knows quite sure what to do with it yet to make it truly essential.