I don't think we have enough detail about Thunderbolt 3 yet to know whether devices will be able to detect that they are connected to a USB port and not a Thunderbolt port. If they can detect that, they may well be able to choose to degrade.
It seems like an ideal way for Apple to be able to ship a display which can be connected to both thunderbolt and USB-C hosts, without the user having to care.
Obviously some Thunderbolt devices (e.g. PCI-E chassis) wouldn't reasonably be able to degrade to USB, but a good proportion of them, would.
I very much hope this is what is going to happen!