Dec 26 19:37:17 tomodachi hub 1-0:1.0: over-current change on port 5Dec 26 19:37:22 tomodachi hub 4-0:1.0: over-current change on port 1Dec 26 19:37:22 tomodachi hub 1-0:1.0: over-current change on port 5Dec 26 19:37:24 tomodachi hub 1-0:1.0: connect-debounce failed, port 5 disabled
that just sounds like your computer disconnected Arduino from the USB bus because it thinks Arduino is drawing too much current... try a different USB port, some are only meant for low current, especially keyboard USB ports.
I haven't seen anything in the foums about buring out USB ports by plugging an Arduino in.. but a quick google search of "over-current change on port" comes up with 15 pages of results for that exact phrase, mostly about hardware-linux conflicts... have a look, it would be much more llikely that Linux is shutting down the port for some reason than that the Arduino had damaged it.
The thing worked fine in the tests, but I suffered the world famous demo effect. And my USB ports stopped working for a while. And when I say for a while, I mean completely and for about a week. Then, the same way they left me, they came back. I was running XP and had only 3 USB port in my laptop.
I vote for the OS blocking a port as the most likely thing to happen to you right now.
"The host and all self-powered hubs must implement over-current protection for safety reasons, and the hub must have a way to detect the over-current condition and report it to the USB software. Should the aggregate current drawn by a gang of downstream facing ports exceed a preset value, the over-current protection circuit removes or reduces power from all affected downstream facing ports. The over-current condition is reported through the hub to Host Controller, as described in Section 11.12.5. ... If an over-current condition occurs on any port, subsequent operation of the USB is not guaranteed, and once the condition is removed, it may be necessary to reinitialize the bus as would be done upon power-up. The over-current limiting mechanism must be resettable without user mechanical intervention. Polymeric PTCs and solid-state switches are examples of methods, which can be used for over-current limiting."
actually it is possible for the port to be 'self healing', believe it or not! This is from the offical specification for USB 2.0.. note the "polymeric PTC's", which are resetable 'self-healing' fuses.
PS: If you are really worried about burning a USB port, you could build a cable with a 1A fuse/PCT in series with the 5V supply: just break open a USB cable and solder it in series with the +5V line. I've never seen a cable like this though, since the official spec as above requires this inside the machine. Or, just use a powered hub between the arduino and the laptop-- one that has the spec'd overcurrent protection.