Personally I wouldn't protect them as the USB connectors pair comes apart easily rather than either causing a trip hazard which might cause personal injury OR risk knocking or transferring shock loads into your equipment at one or both ends of the cable. The fact that they are coming undone suggests there's enough stress on the cable to risk damaging something

If you feel that you must use a very long cable then you should look at one cable to run the whole length (including being taped to the floor.) That may mean grabbing some Cat5 Shielded cable and making your own long cable, picking USB baluns or using a USB over IP solution where you can use Cat5 cable and make your own to length (there are instructables on it). It won't meet USB spec but according to comments you're well over that anyway so it shouldn't matter.

You can also hook up a device like a Raspberry Pi (other systems are available) with USBIP or IncentivesPro and share the USB port in software from that device to your target. That would allow you to put your USB device on the end of a wireless-n adapter (say a 5GHz one to avoid interference from other kit) and not worry about wires at all.

Or Duct Tape... Duct Tape is always a solution, except when the solution is WD40.