My comment had nothing to do with Bluetooth vs. USB comparison. I only said Bluetooth is a transport layer and claiming it's "notoriously bad security" is not all that correct since most of the security parts come on top of it. So in many ways Bluetooth is quite similar to TCP, at least from point of communication. From the software point of view, both with Bluetooth and TCP, you create a socket then send and receive data through it. Literally the same interface. Protecting data that goes through either method is meant to be done at that point be it with encryption, identity verification, whatever.
Same thing applies to USB, but being physical it has added benefit of having to connect to it but that opens whole set of new potential issues. So it's easier to physically protect it, but should that protection fail, you might end up in even more trouble.