I've had this same error "Error in usb_bulk_read: -110". It seems to be specific to the host you are running the script on, but I haven't found a definite answer as to why.
I'd recommend switching to another computer with different USB ports and run the script there. I was having problems with Ubuntu 12.04 on an Asus Desktop board, then switched to Crunchbang with Debian 7.7 on an Asus EeePC 1000. The problem went away, although I want to point out that the instructions are need to been very specific in the order that you do things: 1) run the script first, then 2) connect the Nest Thermostat, and then 3) reboot the Thermostat by holding down it's screen/button for 10 seconds.
Maybe it's something to do with the USB host controller or a bad cable, but it does read the device, so I can't understand it.
Other things to ensure is that you're using a 32-bit system or a 64-bit system on the host. It's been mentioned that it can have an impact, depending on instruction sets when compiling the images for the Thermostat.